All posts by Elena Dreosti

Experimental Neuroscience Bootcamp 2024

This is a Cajal NeuroKit course that combines online lectures on fundamentals and advanced neuroscience topics with hands-on and physical experiments. Researchers can participate from anywhere in the world because the course material is shipped to participants in a kit box that contains all the tools needed to follow the online course.

Course overview

This course provides a fundamental foundation in the modern techniques of experimental neuroscience. It introduces the essentials of sensors, motor control, microcontrollers, programming, data analysis, and machine learning by guiding students through the “hands on” construction of an increasingly capable robot.

In parallel, related concepts in neuroscience are introduced as nature’s solution to the challenges students encounter while designing and building their own intelligent system.

Course Partners

What will you learn?

The techniques of experimental neuroscience advance at an incredible pace. They incorporate developments from many different fields, requiring new researchers to acquire a broad range of skills and expertise (from building electronic hardware to designing optical systems to training deep neural networks). This overwhelming task encourages students to move quickly, but often by skipping over some essential underlying knowledge.

This course was designed to fill-in these knowledge gaps.

By building a robot, you will learn both how the individual technologies work and how to combine them together into a complete system. It is this broad-but-integrated understanding of modern technology that will help students of this course design novel state-of-the-art neuroscience experiments.

Course directors

Adam Kampff

Course Director
Voight Kampff, London, UK

Andreas Kist

Course Director
Department for Artificial Intelligence in Biomedical Engineering (AIBE), Erlangen, Germany

Elena Dreosti

Co-Director
University College London, UK

Programme

Day 1 – Sensors and Motors

What will you learn?

You will learn the basics of analog and digital electronics by building circuits for sensing the environment and controlling movement. These circuits will be used to construct the foundation of your course robot; a Braitenberg Vehicle that uses simple “algorithms” to generate surprisingly complex behaviour.

Topics and Tasks:

  • Electronics (voltage, resistors, Ohm’s law): Build a voltage divider

  • Sensing (light-dependent resistors, thermistors): Build a light/temperature sensor

  • Movement (electro-magentism, DC motors, gears): Mount and spin your motors

  • Amplifying (transistors, op-amps): Build a light-controlled motor

  • Basic Behaviour: Build a Braitenberg Vehicle

Day 2: Microcontrollers and Programming

What will you learn?

You will learn how simple digital circuits (logic gates, memory registers, etc.) can be assembled into a (programmable) computer. You will then attach a microcontroller to your course robot, connect it to sensors and motors, and begin to write programs that extend your robot’s behavioural ability.

Topics and Tasks:

  • Logic and Memory: Build a logic circuit and a flip-flop

  • Processors: Setup a microcontroller and attach inputs and outputs

  • Programming: Program a microcontroller (control flow, timers, digital IO, analog IO)

  • Intermediate behaviour: Design a state machine to control your course robot

Day 3: Computers and Programming

What will you learn?

You will learn how a modern computer’s “operating system” (Linux) coordinates the execution of internal and external tasks, and how to communicate over a network (using WiFi). You will then use Python to write a “remote-control” system for your course robot by developing your own communication protocol between your robot’s linux computer and microcontroller.

Topics and Tasks:

  • Operating Systems: Setup a Linux computer (Raspberry Pi)

  • Networking: Remotely access a computer (SSH via WiFi)

  • Programming: Program a Linux computer (Python)

  • Advanced behaviour: Build a remote control robot

Day 4: (Machine) Vision

What will you learn?

You will learn how grayscale and color images emerge and how to work with them in a Python environment. By mounting a camera on your robot, you can live-stream the images to your computer. You will then use background subtraction and thresholding to program an image-based motion detector. You will use image moments to detect and follow a moving light source, and learn about “classical” face detection.

Topics and Tasks:

  • Images: Open, modify, and save images

  • Camera: Attach and stream a camera image

  • Image processing: Determine differences in images

  • Pattern recognition: Extract features from images

Day 5: (Machine) Learning

What will you learn?

You will learn about modern deep neural networks and how they are applied in image processing. You will extend the intelligence for your robot, by adding a neural accelerator to the robot. We will deploy a deep neural network for face detection and compare it to the “classical” face detector. Ultimately, you will create and train your own deep neural network that will allow your robot to identify it’s creator, you.

Topics and Tasks:

  • Inference: Implement a neural accelerator (Google Coral USB EdgeTPU)

  • Deployment: Deploy and run a deep neural network

  • Object detection: Finding faces using a deep neural network (Single Shot Detector)

  • Object classification: Train a deep neural network to identify one’s own face (TF/Keras)

The course will be held from 14:00 to 18:00 CET

Registration

Registration fee: 500€ per person (includes shipping of the course kit, pre-recorded and live lectures before and during the course, full attendance to the course, and course certificate).

Registration fee for a group: 500for one person and one course kit + 150€ per additional person (without the course kit)

Applications are closed but you can express your interest in this course, by using the form above. We will contact you when the applications re-open.

To receive more information about this NeuroKit, email info@cajal-training.org

Sponsors

Supported by a gift from the Simons Foundation

Neuro-vascular function in health and disease

Course overview

The neurovascular unit, composed of vascular cells, glial cells, and neurons is fundamental for the proper function of the brain. The NVU regulates supply of the cerebral blood flow (CBF) and maintains integrity of the blood-brain barrier (BBB).

Dysfunction of the neurovascular unit may result in devastating conditions such as dementia, cerebral ischemia, or brain oedema formation. This advanced experimental course will allow students to gain basic knowledge and hands-on experience on the most important techniques used to study the neurovascular unit, such as in vivo/in vitro high-resolution imaging, magnetic resonance imaging, and rodent models of cerebrovascular disease. The course will also focus on data reproducibility and open science.

Course partner

Course directors

Nikolaus Plesnila

Course Director

Ludwig Maximilian University, Germany

Jérôme Badaut

Course Director

Bordeaux University, France

Catherine Hall

Course Director

Sussex University, UK

Keynote Speakers

David Attwell – University College London, UK
Felipe Barros – Centro de Estudios Científicos, Chile
Serge Charpak – University of Paris, France
Turgay Dalkara – Hateceppe University, Turkey
Ali Ertürk – University of Munich, Germany
Jean Francois Ghersi-Egea – Lyon Neuroscience Research Centre, France
Anne Joutel – University of Paris, France
Martin Lauritzen – University of Copenhagen, Denmark
Malcolm MacLeod – University of Edinburgh, UK
Pierre Magistretti – University of Lausanne, Switzerland
Maiken Nedergaard – University of Copenhagen, Denmark
Mark Nelson – University of Burlington, USA
Andy Obenhaus – USI, USA
Andy Shih – Seattle Children’s Research Institute, USA
Robert Thorne – Denali Therapeutics / University of Wisconsin-Madison, USA
Susanne Van Veluw – Harvard Medical School, USA

Instructors

Silvia Anderle – University of Sheffield
Orla Bonnar – University of Sheffield
Gian-Marco Calandra – Massachusetts General Hospital
Audrey Chagnot – University of Sussex
Yulia Dembitskaia – University of Edinburgh
Maximillian Dorok – Johns Hopkins
Christophe Dubois – université de Bordeaux
Beth Eyre – University of Munich
Severin Filser – University of Munich
Jordan Girard – Université de Bordeaux
Clare Howarth – University of Munich
Malika Ihle – University of Munich
Igor Khalin – University of Munich
Tom Langdon – University of Munich
Guillaume Le Bourdelles – Inscopix
Axel Montagne – Université de Bordeaux
Burcu Seker – Université de Bordeaux
Josh Shrouder – University of Munich
Rebecca Sienel – University of Edinburgh
Jonathan Zapata – Johns Hopkins

Course content

This 3-week long course is a practical “hands-on” introduction to advanced methods for the investigation of the neuro-vascular unit in health and disease. The course will be structured in a theoretical and a practical part.

In the theoretical part world leading scientists in the neurovascular unit (NVU) research will give overview lectures about the function of the NVU and present techniques how to study the NVU in a reproducible manner. Such overview presentations will be paralleled by workshops. In the practical part of the course students will learn surgical techniques necessary to perform animal models of disease and to prepare cranial windows required for the study of cerebral vessels, will be trained to image cerebral vessel function in vitro and in vivo, and will learn how to analyse and display the acquired data.

Techniques

The following techniques will be taught at the course:

  • Chronic cranial window surgery

  • Habituation to the rig for awake imaging

  • Experimental design and presentation of stimuli

  • 2 photon imaging of neurovascular coupling (neuronal activity, blood vessel dilations)

  • 2 photon imaging of vascular function (vasomotion, calcium signals in vessels)

  • Wide field imaging and recording of neurovascular function and metabolism (2D OIS, laser speckle, haemoglobin spectrometry, laser doppler flowmetry – equipment to be loaned by Moor Instruments)

  • Data processing and analysis

Projects

The following projects will be taught at the course:

  • Two-photon microscopy imaging of blood vessels and neuronal activity in vivo

  • Brain imaging in freely moving mice using mini-scopes

  • Two-photon microscopy imaging of stroke

  • Widefield imaging of neurovascular relationships

  • Open Science

  • Correlative light-electron microscopy (CLEM)

  • Vascular signalling in pressurized brain slices

  • BBB permeability in mice and humans by MRI

  • SUSHI – evaluating the brain’s extracellular space by STED microscopy

  • Histological techniques for the analysis of cerebral vessels

  • Brain clearing for the analysis of cerebral vessels

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 : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed on 14 November 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
UK

Susana Lima

Course Director
Portugal

Tiago Branco

Course Director
UK

Executive director

Pedro Garcia da Silva

Course Executive Director
Portugal

Keynote Speakers

Instructors

Stan Heinze – Lund University, Sweden
Chris Xu
Cornell University, USA
Michael Orger – Champalimaud Foundation, Portugal
Constanze Lenschow
– Magdeburg University, Germany
Ana João Rodrigues
– ICVS, Minho University, Portugal
Bob Datta
– Harvard University, USA
Marta Moita
– Champalimaud Foundation, Portugal
Botond Roska – Institute of Molecular and Clinical Ophthalmology Basel, Switzerland
Tobias Rose – University of Bonn Medical Center, Germany
Darcy Peterka
– Columbia University, USA
Vanessa Ruta –
Rockefeller University, USA
Eugenia ChiappeChampalimaud Foundation, Portugal
Isaac Bianco
University College of London, UK
Christine Constantinople
– New York University, USA
Nicolò Accanto
– Institut de la Vision, France
Carsen Stringer
– HHMI Janelia, USA
Greg Jefferis
– MRC Laboratory of Molecular Biology, UK
Nick Steinmetz
– University of Washington, USA
Michael Brecht
– Bernstein Center for Computational Neuroscience, Germany

Course content

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.

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 : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed on 31 January 2023

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

Supported by a gift from the Simons Foundation

Experimental Neuroscience Bootcamp 2023

Applications are closed but you can express your interest in this course, by using the form above. We will contact you when the applications re-open.

This is a Cajal NeuroKit course that combines online lectures on fundamentals and advanced neuroscience topics with hands-on and physical experiments. Researchers can participate from anywhere in the world because the course material is shipped to participants in a kit box that contains all the tools needed to follow the online course.

Course overview

This course provides a fundamental foundation in the modern techniques of experimental neuroscience. It introduces the essentials of sensors, motor control, microcontrollers, programming, data analysis, and machine learning by guiding students through the “hands on” construction of an increasingly capable robot.

In parallel, related concepts in neuroscience are introduced as nature’s solution to the challenges students encounter while designing and building their own intelligent system.

Course Partners

What will you learn?

The techniques of experimental neuroscience advance at an incredible pace. They incorporate developments from many different fields, requiring new researchers to acquire a broad range of skills and expertise (from building electronic hardware to designing optical systems to training deep neural networks). This overwhelming task encourages students to move quickly, but often by skipping over some essential underlying knowledge.

This course was designed to fill-in these knowledge gaps.

By building a robot, you will learn both how the individual technologies work and how to combine them together into a complete system. It is this broad-but-integrated understanding of modern technology that will help students of this course design novel state-of-the-art neuroscience experiments.

Course directors

Adam Kampff

Course Director
Voight Kampff, London, UK

Andreas Kist

Course Director
Department for Artificial Intelligence in Biomedical Engineering (AIBE), Erlangen, Germany

Elena Dreosti

Co-Director
University College London, UK

Programme

Day 1 – Sensors and Motors

What will you learn?

You will learn the basics of analog and digital electronics by building circuits for sensing the environment and controlling movement. These circuits will be used to construct the foundation of your course robot; a Braitenberg Vehicle that uses simple “algorithms” to generate surprisingly complex behaviour.

Topics and Tasks:

  • Electronics (voltage, resistors, Ohm’s law): Build a voltage divider

  • Sensing (light-dependent resistors, thermistors): Build a light/temperature sensor

  • Movement (electro-magentism, DC motors, gears): Mount and spin your motors

  • Amplifying (transistors, op-amps): Build a light-controlled motor

  • Basic Behaviour: Build a Braitenberg Vehicle

Day 2: Microcontrollers and Programming

What will you learn?

You will learn how simple digital circuits (logic gates, memory registers, etc.) can be assembled into a (programmable) computer. You will then attach a microcontroller to your course robot, connect it to sensors and motors, and begin to write programs that extend your robot’s behavioural ability.

Topics and Tasks:

  • Logic and Memory: Build a logic circuit and a flip-flop

  • Processors: Setup a microcontroller and attach inputs and outputs

  • Programming: Program a microcontroller (control flow, timers, digital IO, analog IO)

  • Intermediate behaviour: Design a state machine to control your course robot

Day 3: Computers and Programming

What will you learn?

You will learn how a modern computer’s “operating system” (Linux) coordinates the execution of internal and external tasks, and how to communicate over a network (using WiFi). You will then use Python to write a “remote-control” system for your course robot by developing your own communication protocol between your robot’s linux computer and microcontroller.

Topics and Tasks:

  • Operating Systems: Setup a Linux computer (Raspberry Pi)

  • Networking: Remotely access a computer (SSH via WiFi)

  • Programming: Program a Linux computer (Python)

  • Advanced behaviour: Build a remote control robot

Day 4: (Machine) Vision

What will you learn?

You will learn how grayscale and color images emerge and how to work with them in a Python environment. By mounting a camera on your robot, you can live-stream the images to your computer. You will then use background subtraction and thresholding to program an image-based motion detector. You will use image moments to detect and follow a moving light source, and learn about “classical” face detection.

Topics and Tasks:

  • Images: Open, modify, and save images

  • Camera: Attach and stream a camera image

  • Image processing: Determine differences in images

  • Pattern recognition: Extract features from images

Day 5: (Machine) Learning

What will you learn?

You will learn about modern deep neural networks and how they are applied in image processing. You will extend the intelligence for your robot, by adding a neural accelerator to the robot. We will deploy a deep neural network for face detection and compare it to the “classical” face detector. Ultimately, you will create and train your own deep neural network that will allow your robot to identify it’s creator, you.

Topics and Tasks:

  • Inference: Implement a neural accelerator (Google Coral USB EdgeTPU)

  • Deployment: Deploy and run a deep neural network

  • Object detection: Finding faces using a deep neural network (Single Shot Detector)

  • Object classification: Train a deep neural network to identify one’s own face (TF/Keras)

The course will be held from 14:00 to 18:00 CET

Registration

Registration fee: 500€ per person (includes shipping of the course kit, pre-recorded and live lectures before and during the course, full attendance to the course, and course certificate).

Registration fee for a group: 500for one person and one course kit + 150€ per additional person (without the course kit)

Applications are closed but you can express your interest in this course, by using the form above. We will contact you when the applications re-open.

To receive more information about this NeuroKit, email info@cajal-training.org

Sponsors

Supported by a gift from the Simons Foundation

Glial cells in health and diseases

Course overview

For over a century, the main focus of neuroscience research has been on neurons. It is however, becoming ever more clear that brain functions such as conceptual reasoning, memory, and processing speed depend on glial cells (microglia, astrocytes and oligodendrocytes).

The lack of understanding of the role of glia in normal brain development, function and disease is mainly due to lack of tools and methods to accurately study these cells. In recent years, neuroscience has seen a methodological revolution. The function of glia cells in neuronal circuit development, and neurodegenerative disease has become evident. The study of glial biology and the understanding on how glial cells impact on circuit function are key to understanding how the brain works and what goes wrong in brain disease. Advanced training of a new generation of neuroscientists with strong focus on glial function is crucial to make these studies a success in the coming decades.

Course directors

Cambridge University, UK

Cagla Eroglu

Course Director

Duke University, US

Staci Bilbo

Course Director

Duke University, US

Bordeaux Neurocampus, FR

Keynote Speakers

Amit Agarwal – Heidelberg University, Germany
Paola Arlotta – Harvard University, US
David Belin – University of Cambridge, UK
Bart J. L. Eggen – University Medical Center Groningen, The Netherlands
Sonia Garel – Institut de Biologie de l’Ecole Normale Superieure (IBENS), Paris, France
Soyon Hong – UCL, London, UK
Maarten Kole – Utrecht University, The Netherlands
Kelly Monk – The Vollum Institute, OHSU, US
Stéphane Oliet – Neurocentre Magendie, France
Thomas Papouin – Washington University School of Medicine in St. Louis, US
Nathalie Rouach – College de France, France
David Rowitch – University of Cambridge, UK
Mikael Simons – Technical University Munich, Germany

Instructors

Amit Agarwal – Heidelberg University, Germany
Liam BarryCarroll – IMN, Bordeaux Neurocampus, France
Arne Battefeld – IMN, Bordeaux Neurocampus, France
Felipe Bodaleo – Heidelberg University, Germany
Sarah Bou Sader Nehme – IMN, Bordeaux Neurocampus, France
Sara Carracedo Vicente – IMN, Bordeaux Neurocampus, France
Omar De Faria – Stem Cell Institute, University of Cambridge, UK
Mohit Dubey – Netherlands Institute for Neuroscience, The Netherlands
Jiaxing Li – Oregon Health & Science University, US
Charlotte Madore-Delpech – INRAE, University of Bordeaux, France
Giampaolo Milior – College de France, France
Wiebke Möbius – Max Planck Institute for Multidisciplinary Sciences, Germany
Torben Ruhwedel – Max Planck Institute for Multidisciplinary Sciences, Germany
Kristina Sakers Hays – Duke University Medical Center, US
Caroline Smith – Boston College, US
Francesco Ulloa Severino – Duke University, US

Course content

This is a theoretical and practical training course on glial cells and their communication with neuronal circuits. It will provide an overview of the current concepts and knowledge of glial cell biology in central and peripheral nervous system development in several species, including zebrafish, mice, and humans, and their link to diseases.

It will combine lectures and hands-on projects on glial development including methods in cellular neuroscience (e.g. live and fixed tissue imaging), genetic modifications, -omics (e.g., scRNA seq, proteomics and bioinformatics), electrophysiology, optogenetic and chemogenetic manipulation of glial cells and methods to study behaviour.

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.

Sponsors

Registration

Fee : 3.950 € (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.

Machine learning for neuroscience

Course overview

Neuroscience has played an important role in the history of Artificial intelligence and Machine learning. Artificial neural networks are inspired by neuronal physiology and are today the core of Deep Learning. This common history continues today. Machine Learning methods are developed into tools that allow for a higher quality of data processing in the study of animal behavior and brain activity. Machine Learning is also used to model the brain as it can solve similar problems to what brains solve and the basic units of processing may be comparable.

The course gives a hands-on introduction to Artificial Intelligence and Machine Learning and how it can be used for data acquisition, analysis and modeling brain activity and behavior. Experts in the field will teach the basics of Machine Learning and how to apply it to Neuroscience and will also discuss the limits of the field, and what are the boundaries of application and how Neuroscience and Psychology could inform new systems.

Course directors

Gonzalo de Polavieja

Course Director

Champalimaud Foundation, PT

Kristin Branson

Course Director

HHMI Janelia, USA

Il Memming Park

Course Director

Champalimaud Foundation, PT

Keynote Speakers

Ann Kennedy – Northwestern University, US
N. Alex Cayco Gajic – École Normale Supérieure, France
Ben Cowley – Cold Spring Harbor, US
Kim Stachenfeld – DeepMind, UK
Jennifer Sun Caltech, US
Josue Nassar – Stony Brook University, US
Laura Driscoll – Stanford University, US
Maneesh Sahani Gatsby Computational Neuroscience Unit, UK
Nakul Verma – Columbia University, US
Patrick Mineault – xcorr, Canada
Rui Ponte Costa – University of Oxford, UK
Sara Solla – Northwestern University, US
Surya Ganguli Stanford University, US

Instructors

Course content

Programme

During the first two weeks, there will be lectures in the morning, and evening tutorials will consist of analytical and computational application of the concepts learned in the morning. The third week consists of lectures in the mornings and projects in the evening.

First week

The first week will consist of a mini-course in Machine Learning, especially those techniques used in Neuroscience. This will include supervised and unsupervised learning, learning for time series and Reinforcement Learning, as well as a day dedicated to practical aspects in the use of Machine Learning Techniques.

Day 1: History of AI and the relationship between Machine Learning and Neuroscience
Day 2: Supervised Learning
Day 3: Unsupervised Learning
Day 4: Practical consideration of the use of Machine Learning
Day 5: Learning for Time Series
Day 6: Reinforcement Learning

Second Week

The second week discusses how Machine Learning techniques are applied in Neuroscience. This will include the Machine Learning tools used to extract information from datasets of animal behavior and brain activity, Machine Learning models from brain activity and behavior, models using spiking neural networks and which are the limits ofML techniques.

Day 7: ML tools in animal behavior
Day 8: ML tools in brain activity
Day 9: Models derived from the brain and behavior
Day 10: ML-based models of the brain & discrepancies
Day 11: Theory-based modeling, and its connection to ML
Day 12: Bio-inspired ML/spiking networks

Third week

The third week has lectures on more advanced topics and evenings on projects.

Students will design projects applying machine learning (ML) methods to neural recording and animal behavior data sets. Neural recording data sets provided will be from a variety of techniques, including electrophysiology, calcium imaging, and fMRI. Behavior data sets provided will be from video. Students may focus on developing new ML algorithms for improving automated tracking, segmentation, categorization, or representation learning. Alternatively, they may focus on applying these ML methods to large data sets to discover new biological insights. A third option is to explore ML-based computational models of neural activity or behavior. Through these projects, students will gain hands-on experience using modern ML approaches, coding in PyTorch, and gain a deeper understanding of the power and potential failures of ML.

Datasets

Behavioral Datasets

  • Fish Fish in groups, raw and tracked
  • Some rodents and ants, raw and tracked
  • Flies data from Maabe and other datasets.

Neural Datasets (spike trains)

  • Neural Latent Benchmark ones
  • Neuromatch ones (e.g. Steinmetz)
  • Brain machine interface related datasets
  • IBL datasets

Other Neural Datasets ( LFP, fMRI, etc)

Computational models (not datasets but used as input for further analysis or modeling)

  • RNNs trained on tasks
  • Models trained on fish in collectives

Techniques

  • Deep learning tools for analyzing complex behavior data

  • Neural manifolds

  • Modeling neural computation with recurrent neural networks

  • State space modeling of neural time series

  • Probabilistic modeling of neural data and behavior

  • Deep learning models of brain activity and behavior

  • Spiking neural networks

  • Best practices for high quality neuroscience research using machine learning

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 : €2.950,00 (includes tuition fee, accommodation and meals)

Applications closed on 23rd January 2023

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

Extracellular Electrophysiology Acquisition 1023

This is a Cajal NeuroKit course that combines online lectures about fundamentals and advanced neuroscience topics with hands-on and physical experiments.

Researchers from everywhere can participate because the course material is sent home in a kit box.

This course is now at its third edition.

Course overview

Any data we collect has been shaped by the system we used to record it. Understanding the tools involved in data acquisition gives you the confidence to make informed experimental design choices, and the freedom to combine and try new approaches while building your dream setup.

In this course, we will develop your understanding of electrophysiology data acquisition. In terms of hardware, you will learn how acquisition systems can amplify tiny signals and filter out noise. You’ll test this understanding by building your own system to measure muscle and heart signals. In software, you will encounter synchronisation considerations, as we add incoming datastreams and build an increasingly complex experimental design.

Don’t be discouraged if you secretly panic at the mention of capacitance, this course starts from the very basics. Advanced students can make the final project as challenging as they like.

Designed by Open Ephys and Open Ephys Production Site, this course will have an open-source flavour and encourage you to try new ideas, share your insights, and connect with the open-source community.

Course sponsors

What will you learn?

By the end of the course, you will:

  • be familiar with the electronic building blocks of acquisition systems

  • be able to model and build circuits to amplify and filter incoming signals

  • be able to use the Bonsai programming language to stream data and run closed-loop experiments with multiple datastreams

Course Directors

Cecilia Herbert

Course Director

Open Ephys Production Site, PT

Jakob Voigts

Course Director

MIT and Open Ephys, USA

Filipe Carvalho

Course co-director

Open Ephys Production Site, PT

Guest video lecturers

– Alex Leighton, Open Ephys Production Site, PT

– Joana Neto, FCT NOVA, PT

– Jakob Voigts, Janelia Research Campus and Open Ephys, USA

-Filipe Carvalho, Open Ephys Production Site, PT

Teaching Assistants

Every year we have an amazing group of Teaching Assistants who remotely help the students as they work on the course activities. Past TAs have been selected from institutes such as Champalimaud Foundation in Portugal, The Francis Crick Institute in the UK and the University of Buenos Aires in Argentina.

Course designers

This course was brought to life thanks to the remarkable work of Alex Leighton as course director for the first three editions, with the vision of course director Jakob Voigts and co-director Filipe Carvalho and the help of Aarón Cuevas López (Universitat Politècnica de València, ES and Open Ephys Production Site, PT), Joana Neto (FCT NOVA, PT), Jonathan P. Newman (MIT and Open Ephys, USA) and Josh Siegle (Allen Institute, USA).

Programme

Day 1 – Introduction

  • What are we trying to measure? Electrical signals in the brain and ways to record them.

  • How can we collect these signals without changing them? Considerations when building an acquisition system.

  • Using a simulator to visualise electrical circuits online and make predictions about real-world circuits.

  • Using the breadboard and components in your kit to test your understanding of electronics concepts.

Day 2 – Impedance

  • Using microcontrollers to acquire physiological data.

  • What is impedance? Understanding how we protect our signals while measuring them.

  • Understanding the function and limitations of operational amplifiers.

Cajal Images -Day 1
Cajal- Day 3

Day 3 – Data Acquisition

  • Understanding Instrumentation Amplifiers.

  • Simulating, building and testing low & high-pass filters.

  • Visualise your own EMG/ECG data using the Bonsai programming language.

Day 4 – Synchronizing Datastreams

  • Expanding on Bonsai – controlling cameras, receiving other datastreams.

  • Understanding closed-loop experiments, timestamp considerations, and synchronising datastreams.

  • Designing student projects and group feedback on plan.

Day 5 – Project and Open-Source Neuroscience

  • Open Ephys – open-source hardware & software development.

  • An overview of open-source community projects.

  • Student project presentation.

Cajal- Day 4

The course will be held from 14:00 to 18:00 GMT.

Registration

Registration fee: 500€ per person (includes shipping of the course kit, pre-recorded and live lectures before and during the course, full attendance to the course, and course certificate).

Registration fee for a group: 500€ for one person and one course kit + 150€ per additional person (without the course kit). For this course, groups can be up to 3 persons maximum sharing  1 single kit.

To receive more information about this NeuroKit, email info@cajal-training.org

Connectomics from micro- to meso- and macro-scales

Course overview

The biological factors shaping the synaptic connectivity of neuronal circuits are complex and multifaceted, depending on cell types, functional activity, homeostasis, and more. Mapping brain wiring at the level of both local circuits and across brain-wide projections is a key aspect of understanding how nervous systems develop, learn, process information and generate behaviour. Recent advances in molecular biology, tissue processing, computational methods, and microscopy have enabled a revolution in understanding structural connectivity with cellular and synaptic resolution. Large-scale electron microscopy volumes provide nanometer-scale maps of anatomy and connectivity of whole invertebrate brains and millimetre-scale regions of vertebrate brains, while light-microscopic methods can highlight genetically defined connections and enable brain-wide reconstruction of neurons. Together, these complementary approaches yield powerful insight into the neuroanatomy and connectivity of the nervous system with single-cell resolution.

This course will provide students with a broad introduction to contemporary methods of studying neuronal connectivity with lectures from experts in the field. It also provides practical project-based instruction in experimental methods of circuit tracing and reconstruction with light microscopy (light sheet or 2-photon), as well as the computational analysis of rich electron microscopy connectomes in flies and mice. Students will consider the strengths and limitations of different techniques and how they can be used to address key problems in circuit neuroscience.

Course directors

Gregory Jefferis

Course Director

MRC LMB and University of Cambridge, UK

Jinny Kim

Course Director

Korea Institute of Science and Technology, Korea

Nicolas Renier

Course Director

Paris Brain Institute, France

Allen Institute of Brain Science, US

Keynote Speakers

Jae-Byum Chang – KAIST, South Korea
Christel Genoud – University of Lausanne, Switzerland
Moritz Hemlstaedter – Max Plank Institute for Brain Research, Germany
Valentin Nägerl – University of Bordeaux, France
Alexandra Pacureanu – European Synchrotron Radiation Facility, France
Hiroki Ueda – Laboratory for Synthetic Biology, Japan
Claire Wyart – ICM Institute for Brain and Spinal Cord, France
Johannes Kohl – The Crick Institute, UK
Constantin Pape – University of Göttingen

Instructors / Teaching Assistants

Alba Vieites Prado – Universitad de Santiago de Compostela
Andrew Champion – Cambridge University, UK
Fabian Voigt – Harvard University, USA
In Cho – KAIST, Korean Advance Institute of Science and Technology, Korea
Jihyun Kim – KIST, Korean Institute of Science and Technology, Korea
Jordan Girard – université de Bordeaux
Katharina Eichler – Leipzig University, Germany
Leila Elabbady – University of Washington.
Martin Carbo-Tano – Paris Brain Institute, France
Philipp Schlegel – University of Cambridge, UK
Sahil Loomba – Max Planck Institute for Brain Research, Germany
Thomas Topilko – Gubra, Inc
Yagmur Yenner – Max Planck Institute for Brain Research, Germany
Yulia Dembitskaia – Université de Bordeaux

Course content

Light Microscopy and functional, molecular methods:

– Choice of labelling strategy: use of specific cre lines (for instance, the GENSAT project); finding specific markers for cell populations; using viral vectors and intersectional genetics (Dual or triple injections, transsynaptic tracing, Tango system, mGRASP, etc.).

– Tissue preparation for imaging: tissue clearing: choice of methods, considerations for the resolution needed and type of molecular labelling (Ueda, Renier); expansion microscopy methods: when to use them, and which iteration (Jae-Byum Chang)

Imaging strategy: use of scanning microscopes: confocal or 2p, in intact samples or using serial sectioning; use of light sheet microscopy: commercial systems (eg. Miltenyi’s Blaze or Zeiss Z7), and custom systems (Mesospim).

Analysis of imaging data: use of neuron mapping pipelines for whole brain data obtained from light sheet microscopy or from sections (eg. ClearMap, TrailMap, WholeBrain, etc). (Ueda, Renier); se of virtual reality-assisted tools for single neuron reconstructions from 3D datasets (eg. SyGlass, Vision4D…).

Electron microscopy synaptic connectomics:

At the end of this course, the students will be familiar with all of the steps that go into producing and analysing large scale, synaptic resolution EM connectomics datasets, summarised as below. Detailed analysis projects tailored by student interest will use public datasets and open source tools in which their directors and their colleagues are experts. These include the microns mouse cortical cubic millimetre dataset (https://www.microns-explorer.org/) and fly CNS datasets including the hemibrain, flywire.

Techniques

  • EM imaging for connectomics (theory, image analysis)
  • X-ray imaging for connectomics (theory, image analysis)
  • EM connectomics data analysis (detailed hands on coverage for latest public whole brain fly and mouse cortex datasets; other organisms pending)
  • In vivo calcium imaging
  • In vivo 2-photon microscopy
  • Light sheet microscopy
  • Tissue Clearing
  • Expansion Microscopy
  • Brain mapping of cleared tissue (image analysis, commercial and academic softwares)

Projects

  1. Mapping of axonal projections with light sheet microscopy in the mouse brain
  2. Assembly of a Mesospim microscope for whole brain mapping with tissue clearing
  3. Brain mapping of cellular markers with HCR-fish, tissue clearing and light sheet microscopy
  4. In vivo recording of activity and connectivity in the Zebrafish larva
  5. Inference of information flow in Zebrafish larva using calcium imaging and Granger Causality
  6. Microscale connectomic analysis of mammalian connectomics data
  7. Morphological and connectivity analysis of the MICrONs mouse visual cortex dataset
  8. Student interest-led project(s) leveraging public mammalian connectomics data
  9. Whole brain circuit analysis using larval / adult Drosophila connectomes
  10. Student interest-led projects using public Drosophila connectomes
  11. Comparative connectomics: within species using multiple Drosophila datasets or across evolution using multiple public EM connectomes.

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 : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed 17 April 2023

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 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.

Course directors

Ana Luisa Carvalho

Course Director

CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Portugal

Mathieu Letellier

Course Director

IINS, University of Bordeaux, France

Hey-Kyoung Lee

Course Director

The Zanvyl Krieger Mind/Brain Institute, The Johns Hopkins University, USA

Keynote Speakers

Alfredo Kirkwood – Johns Hopkins University, USA
Brian D McCabe – EPFL, Lausanne, Switzerland
Cécile Charrier – Institute of Biology, École Normale Supérieure, France
Christian Lohmann – Netherlands Institute for Neuroscience, Netherlands
Daniel Choquet – IINS, University of Bordeaux, France
Joseph Kittler – University College London, UK
Juan Burrone – King’s College London, UK
Julie Perroy – IGF, University of Montpellier, France
Julijana Gjorgjieva – Max Planck Institute for Brain Research, Germany
Marina Mikhaylova – Humboldt Universität zu Berlin, Germany
Nael Nadif Kasri – Radboudumc Donders Institute for Brain, Cognition and Behaviour, Holland
Noa Lipstein – FMP-Berlin, Germany
Rosa Paolicelli – University of Lausanne, Switzerland

Instructors

Alexy Louis – IINS, Univ of Bordeaux, France

Anne-Claire Compagnion – Univ. Lausanne, Switzerland

Elena Baz-Badillo – IINS, Univ Bordeaux, France

Frederic Gambino – IINS, Univ Bordeaux, France

Joana Ferreira – CNC, Univ Coimbra, Portugal

Julia Bär – Humboldt Universität zu Berlin, Germany

Julien Dupuis – IINS, Univ Bordeaux, France

Kevin Crosby – University of Colorado Denver, Department of Pharmacology, USA

Léa Sarzynski – IINS, Univ Bordeaux, France

Lucille Alonso – IINS, Univ Bordeaux, France

Luís Ribeiro – CNC, Univ Coimbra, Portugal

Margaux Giraudet – IINS, Univ Bordeaux, France

Marie-Lise Jobin – IINS, Univ Bordeaux, France

Marina Hommersom – Radboudumc Donders Institute for Brain, Cognition and Behaviour, Holland

Michelle BridiWest Virginia University, USA

Mónica Santos – CNC, Univ Coimbra, Portugal

Olivier Nicole – IINS, Univ Bordeaux, France

Tamara Buijs – Netherlands Institute for Neuroscience, Netherlands

Vivek Belapurkar – IINS, Univ Bordeaux, France

Course content

Exposure to central topics in synapse biology, and hands-on experience with exciting projects with innovative techniques

The research in synapse biology holds a central place in Neuroscience, as it connects findings in molecular and cellular Neuroscience to the understanding of circuits and behaviour. In addition, synaptopathy is a major pathogenic mechanism in both neuropsychiatric and neurodegenerative disorders. The last decades have brought enormous advances in the methodologies used to study synapses, and which endow researchers with the possibility to bridge from the molecular analyses of synapses to cellular, circuits and behaviour approaches to tackle central questions about how the brain works.

This course provides the opportunity to learn from experts in the field about questions at the forefront of synapse biology, and to obtain hands-on experience with innovative techniques to study synapses. These include gene transfer, live imaging of proteins and signalling molecules (including in vivo 2 photon microscopy), superresolution microscopy for cellular imaging of proteins at excitatory and inhibitory synapses, electrophysiology, animal behaviour and computational methods.

Topics

  1. Synaptic traficking
  2. Synaptogenesis, synapse adhesion and synapse maintenance
  3. Presynaptic mechanisms
  4. Inhibitory synapses
  5. Structural and functional synaptic plasticity
  6. Synaptic integration in neuronal networks
  7. Calcium dynamics and signaling
  8. Microglia in the shaping of neural circuits
  9. Synaptic dysfunction in disease
  10. Synaptic computation
microscopy students

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.

Techniques

  • Whole cell patch clamp recordings in brain slices
  • Patch-seq / RNAseq
  • Co-culture synaptogenic assay
  • Synaptic interactome analysis through proximity-dependent labeling
  • Stereotaxic surgery with cannulae implantation
  • Behavior analysis
  • Confocal time-lapse imaging and FRAP measurements
  • FLIM-FRET measurements for activity sensors
  • Single-molecule tracking and PALM studies
  • Direct stochastic optical reconstruction microscopy (dSTORM)
  • hiPSC culturing and neuronal differentiation
  • MEA recording: Axion Maestro Pro
  • Two photon imaging

Experimental projects:

  • Nanoscale organization of the synapse
  • Superresolution microscopy in the analysis of transsynaptic interactions
  • Interactome of synaptic cell-adhesion molecules
  • Architectural and signalling dynamics at the inhibitory synapse
  • Regulation of inhibitory synaptic transmission by wake-active neuromodulators
  • Measuring spontaneous network activity of human iPSC-derived neurons using micro-electrode arrays
  • Microglia-mediated synapse engulfment
  • Membrane trafficking/endo/exocytosis
  • In vivo imaging of boutons related to behavior
  • Pharmacological modulation of fear extinction
  • Mitochondrial dynamics and dendritic calcium imaging
  • Multimodal profiling of synaptic connectivity through patch-seq
 

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 : 3.950 € (includes tuition fee, accommodation and meals)

Applications closed 29 May 2023

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.

Modern Approaches to Behavioural Analysis

Modern Approaches to Behavioural Analysis is a Cajal NeuroKit. The course will combine online lectures on fundamentals and advanced neuroscience topics with guided data analysis and exercises.

Course overview

The goal of neuroscience is to understand how the nervous system controls behaviour, not only in the simplified environments of the lab, but also in the natural environments for which nervous systems evolved.

In pursuing this goal, neuroscience research is supported by an ever-larger toolbox, ranging from optogenetics to connectomics. However, often these tools are coupled with reductionist approaches for linking nervous systems and behaviour. This course will introduce advanced techniques for measuring and analysing behaviour, as well as three fundamental principles as necessary to understanding biological behaviour: (1) morphology and environment; (2) action-perception closed loops and purpose; and (3) individuality and historical contingencies [1].

[1] Gomez-Marin, A., & Ghazanfar, A. A. (2019). The life of behavior. Neuron, 104(1), 25-36

What will you learn?

This course will emphasize the philosophical and observational skills required to understand behaviour, while also providing training in motion capture technologies and computer vision methods that can assist in the collection and analysis of video recorded behaviour datasets.

Focusing on the tool DeepLabCut, students will analyse either their own original video dataset or datasets of general interest and have the opportunity to practice tracking, pose estimation, action segmentation, kinematic analysis and modeling of behaviour.

By the end of the course, you will:

  • be familiar with modern and historical frameworks for studying the behaviour of living biological systems
  • practice methods for carefully and precisely observing and defining behaviours
  • understand the limits and capabilities of computer vision
  • develop an intuition for how to build experimental setups that can take advantage of tools such as DeepLabCut

Furthermore, this course shares and promotes open source software, and we encourage students to try new ideas, share insights, and connect with the open-source community.

Faculty

Course directors

Alexander Mathis

Course Director EPFL, Switzerland

Danbee Kim

Matter Neuroscience, UK

Course contributors

Nicola Clayton, keynote lecture (Cambridge University, UK)

Ole Kiehn, keynote lecture (Copenhagen University, Denmark)

Johanna T Schultz, guest lecture (USC, Australia)

Caleb Weinberg, guest lecture (Harvard Medical School, USA)

Nacho Sanguinetti, guest lecture (Harvard University, USA)

Local Training Hubs

Some of our instructors will be available to run an onsite version of the course in the cities below. This will be a unique opportunity to get in-person tutoring and to take the course alongside other students.

If you’re in or near one of the listed cities and wish to join the onsite course, please indicate your preferred location at the end of your application form in the “Any additional comment” section.

1. Argentina, Buenos Aires

2. Germany, Bochum

3. Greece, Athens

4. Japan, Okinawa

5. Switzerland, Geneva

6. Rwanda, Kigali

7. United Kingdom, Oxford and London

8. Canada, Toronto

9. Germany, Bochum

10. Spain, Valencia

Apply to be a Teaching Assistant!

If you are interested in becoming a Teaching Assistant for this course, we invite you to FILL OUT THIS FORM by the 2nd of August (deadline extended).

You have the option to choose between being an ONLINE TA or a LOCAL TA.

As an ONLINE TA, you will be responsible for teaching exclusively through online platforms. Alternatively, as a LOCAL TA, you will teach a group of students located near you at a local hub.

Last year we had hubs in Buenos Aires, London, Munich, and Nairobi and we are seeking more hubs.

Here is our Global Reach in 2022 (past participants)

Programme

Day 1 – What is animal behaviour?

  • Historical and current theoretical frameworks for the study of behaviour in living biological systems

  • Practical exercises for training skills in observing and defining behaviours

Day 2 – Tools for modern-day ethology

  • Fundamentals of video recording, computer vision, and deep learning

  • Introduction to DeepLabCut

  • Creating a tailored DeepLabCut model for your data or data shared by us.

Day 3 – Training computers to see as we see

  • Multi-animal tracking

  • Live tracking

  • Evaluating, utilizing and optimizing your DeepLabCut model from day 2

Day 4 – Analysis by eye and by computer

  • Movement kinematics in living biological systems

  • Action segmentation – when does a behaviour start and end?

  • Analyse original video dataset of behaviour

  • Joint neural and behavioral analysis

Day 5 – Working on your data and discussion

  • Advanced DLC topics and potential pitfalls

  • Keep analyzing data and student presentations

The course will be held from 13:00 to 17:00 GMT.

Registration

Registration fee: 200€ per person (includes pre-recorded and live lectures before and during the course, tutoring, and course certificate).

To receive more information about this NeuroKit course, email info@cajal-training.org

Sponsors