All posts by Elena Dreosti

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.

Modern Approaches to Behavioral Analysis

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.

We will run a pre-course in May to train Teaching Assistants who would like to help us to teach this course locally or online. We will open applications soon.

Course overview

The goal of neuroscience is to understand how the nervous system controls behaviour [1], 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. Even though the arrival of deep learning tools for animal tracking has changed the scale at which behavioural data is acquired, the scope of questions that can be addressed with these tools can only be expanded when combined with a more nuanced and context-driven approach to the study of 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 [2].

[1] Preface, W.M. Cowan, Annual Review of Neuroscience 1978, Vol 1

https://doi.org/10.1146/annurev.ne.1.072606.100001

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

Course sponsor

What will you learn?

This course will emphasize the philosophical and observational skills required to understand behaviour, while also providing training in image-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 an original video dataset 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

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.

Interested in teaching? We are hiring TAs!

We are looking for teaching assistants to help develop and deliver this course. TAs will be required to attend the pre-course at EPFL (September 19-23). They will then be paid an honorarium to teach the following courses. If you are interested, please fill out this form by [DEADLINE].

Faculty

Alexander Mathis

Course Director EPFL, Switzerland

Danbee Kim

Course co- director Neurogears, UK

Keynote speakers

Nicola Clayton (Univ Cambridge, UK)

Ole Kiehn (Univ of Copenhagen, Denmark)

Guest Lecturers

Johanna T Schultz – (USC, Australia)

Nacho Sanguinetti (Harvard Univ. USA)

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

  • Create an original video recorded dataset of behaviour (students video record their animal puppet engaged in some kind of behaviour)

Day 3 – Training computers to see as we see

  • Multi-animal tracking

  • Live tracking

  • Prepare original video dataset of behaviour for analysis (students trade original video datasets and train their DLC networks)

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 (students try to figure out what behaviour is being performed by their fellow students)

Day 5 – From individuals to populations

  • How do behaviours of living biological systems generalize?

  • Advanced DLC topics and typical pitfalls

  • Students pool all animal puppet videos and try to train DLC to categorize different behaviours

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.

Applications for Teaching Assistants will open in May 2022

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

Visual Reactive Programming – Bonsai 0121

Visual Reactive Programming – Bonsai is a Cajal NeuroKit. NeuroKits are hybrid courses that combine online lectures about fundamentals and advanced neuroscience topics, with hands-on and physical experiments.
Researchers from all over the world can participate thanks to the course material sent by post in a kit box containing all the tools needed to follow the online course. 

Course overview

Modern neuroscience relies on the combination of multiple technologies to record precise measurements of neural activity and behaviour. Commercially available software for sampling and controlling data acquisition is often too expensive, closed to modification and incompatible with this growing complexity, requiring experimenters to constantly patch together diverse pieces of software.

This course will introduce the basics of the Bonsai programming language, a high-performance, easy to use, and flexible visual environment for designing closed-loop neuroscience experiments combining physiology and behaviour data.

This language has allowed scientists with no previous programming experience to quickly develop and scale-up experimental rigs, and can be used to integrate new open-source hardware and software.

Course Teaser

What will you learn?

By the end of the course you will be able to use Bonsai to:

– create data acquisition and processing pipelines for video and visual stimulation.
– control behavioral task states and run your closed-loop experiments.
– collect data from cameras, microphones, Arduino boards, electrophysiology devices, etc.
– achieve precise synchronization of independent data streams.

The online material will be soon found here.

Faculty

Gonçalo Lopes

Course Director

NeuroGEARS, London, UK​

Instructors

João Frazão Champalimaud Research, Lisbon, PT

Niccolò Bonacchi – International Brain Laboratory, Lisbon, PT

Nicholas Guilbeault – University of Toronto, CA

André Almeida – NeuroGEARS, London, UK

Bruno Cruz – Champalimaud Research, Lisbon, PT

Course sponsors

Programme

Day 1 – Introduction to Bonsai

  • Introduction to Bonsai. What is visual reactive programming.

  • How to measure almost anything with Bonsai (from quantities to bytes).

  • How to control almost anything with Bonsai (from bytes to effects).

  • How to measure/control multiple things at the same time with one computer.

  • Demos and applications: a whirlwind tour of Bonsai.

Day 2 – Cameras, tracking, controllers

  • Measuring behavior using a video.

  • Recording real-time video from multiple cameras.

  • Real-time tracking of colored objects, moving objects and contrasting objects.

  • Measuring behavior using voltages and Arduino.

  • Data synchronization. What frame did the light turn on?

Day 3 – Real-time closed-loop assays

  • What can we learn from closed-loop experiments?

  • Conditional effects. Triggering a stimulus based on video activity.

  • Continuous feedback. Modulate stimulus intensity with speed or distance.

  • Feedback stabilization. Record video centered around a moving object.

  • Measuring closed-loop latency.

Day 4 – Operant behavior tasks

  • Modeling trial sequences: states, events, and side-effects.

  • Driving state transitions with external inputs.

  • Choice, timeouts and conditional logic: the basic building blocks of reaction time, Go/No-Go and 2AFC tasks.

  • Combining real-time and non real-time logic for good measure.

  • Student project brainstorming

Day 5 – Visual stimulation and beyond

  • Interactive visual environments using BonVision.

  • Machine learning for markerless pose estimation using DeepLabCut.

  • Multi-animal tracking and body part feature extraction with BonZeb.

  • Student project presentation.

  • Where to next.

Registration

Fee : 300 € (includes lectures and kit)

Application closed on 20 December 2020.

You are welcome to express your interest in the next Cajal Bonsai NeuroKit. Click on the button in the top banner or here.

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

The Last Black Box

Interested in the Last Black Box course? The course was reshaped into a new NeuroKit called Experimental Neuroscience Bootcamp. Visit the page to learn more and apply now.

The Last Black Box is a Cajal NeuroKit. NeuroKits are hybrid courses that combine online lectures about fundamentals and advanced neuroscience topics, with hands-on and physical experiments.
Researchers from all over the world can participate thanks to the course material sent by post in a kit box containing all the tools needed to follow the online course.

Course overview

This course provides a foundation for new experimental neuroscientists. It is targeted at Master students, PhD students or researchers entering the field from another discipline. It should be considered a “prerequisite” for more advanced training courses in a specialized topic.

The course introduces the essentials of data acquisition/control, data analysis, and machine learning by guiding the 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 Teaser

What will you learn?

You will be building a robot without using any black boxes. The robot’s physical layout mimics the basic anatomy of a (vertebrate) brain, and as you gradually open this course’s 21 “boxes” your robot will evolve into an increasingly sophisticated machine. We thus call this robot the No-Black-Box-Bot or NB3.

The course is divided into three sections (following the anatomy of the brain): hindbrain (reflexes), midbrain (behaviour), and forebrain (intelligence?).

The online material can be found here.

Faculty

Adam Kampff

Course Director
Voight Kampff, London, UK

Elena Dreosti

Co-Director
University College London, UK

Instructors

Spencer Wilson – Sainsbury Wellcome Centre, London, UK

Hande Tunbak – University College London, UK

Virginia Rutten – Sainsbury Wellcome Centre, London, UK

Thomas Ryan – University College London, UK

Course sponsors

Voight-Kampff

Programme

Week 1: Measuring and Moving

Aims:

Students build a basic sensory-motor system (a Braitenberg vehicle) that seeks or avoids light and learn about fundamentals of electronics, sensors/actuators, and amplification.

Schedule:

Day 1: “The White Box” Toolkit, Electrons

Day 2: Magnets + Light, Sensors + Motors

Day 3: Semiconductors

Day 4: Amplifiers

Day 5: Reflexes, NB3 robot demos

Week 2: Computers and Programming

Aims:

Students extend their robot to make decisions based on sensory input and perform basic computations. With the addition of a microcontroller, the students will learn the fundamentals of computers and programming, and the robots will develop more complex behaviours.

Schedule:

Day 1: Decisions, Logic

Day 2: Data, Memory

Day 3: Computers

Day 4: Control

Day 5: Behaviour, NB3 demos

Week 3: Data Analysis and Machine learning

Aims:

Students add a computer and camera to their robot. They then learn how to use neural networks to create an “intelligent” visual system that can identify obstacles, rewards and much more…

Schedule:

Day 1: Hearing + Speech, Vision

Day 2: Learning, Intelligence?

Day 3: NB3 work, NB3 work

Day 4: NB3 work, NB3 work

Day 5: NB3 work, NB3 demos

Registration

Course Fee : 900 €
The registration fee includes the black box kit to build the NB3 robot, the white box containing additional tools, shipment of the boxes, faculty and instructor tutoring for 3 full weeks.

The CAJAL programme offers 2 stipends for the Last Black Box NeuroKit (waived registration fee). 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.

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

They took the Last Black Box NeuroKit

“This course opened a lot of black boxes for me. Everything was new and challenging, and I learned so much! It’s super rewarding to see how our robot evolves during these three weeks and how it turns out by the end of the course.”
Marta Maciel (Cellular and Molecular Biology, University of Coimbra)

“Everything about STEM that I missed from an undergrad degree in maths”
Kevin Huang (BA in Mathematics and MMath, University of Cambridge, US)

“The Bootcamp is an incredible way to put technology together, from the fundamentals of physics to modern computers. Not only by explaining it to the students, but also making the students discover and build each component by themselves.”
Rodrigo Carrasco Davis (Electrical engineering, Universidad de Chile, Chile)

“A completely novel approach to education where to understand is not to recite or regurgitate but instead to build, test, and develop a physical manifestation of all that you learn in this wonderful course.”
Christopher Hall (Cell & Molecular Biology, UC Berkeley, US)

“This course distilled a lot of the practical skills I learned from my 5-year electrical engineering education into an intense but exciting 3-week, hands-on adventure. I think this course should be mandatory for neuroscientists, but also available to anyone! Young children, high school students, professionals who rely on computers for their livelihood without understanding what makes them work, and many others can benefit greatly from a version of this course.”
Ali Haydaroglu (Engineering Science with a major in Electrical and Computer Engineering, University of Toronto, Canada)

Cajal online lecture series: Single Cell Transcriptomics

Course overview

To be able to perform molecular analysis on the scale of single-cells with a throughput of 1000s of cells per experiment opens an unprecedented window into neuroscience and biology. We can now ask questions on how different cell types arise, respond to stimuli or are changed in disorders. The multitude of data also moves molecular biology into a new era in terms of data analysis and statistics, changing the demands on researchers. In this online course, we will hear from some of the leaders in the field in the use of single-cell transcriptomics and the analysis of the nervous system. The aim is to cover a wide range of aspects from chemistries and methodologies of single cell transcriptomics to computational methods to leverage this new wealth of data to push our understanding of the brain.

Jens Hjerling-Leffler

Co-Director

Karolinska Institute, Sweden

Peter Kharchenko

Co-Director

Harvard Medical School, USA

Keynote Speakers

Naomi Habib – Edmond & Lily Safra Center for Brain Sciences (ELSC), Israel

Kenneth Harris – University College London (UCL), UK

Ed Lein – Allen Institute for Brain Science, US

Sten Linnarsson – Karolinska Institute, Sweden

John Marioni – European Bioinformatics Institute (EMBL-EBI), UK

Ana Martin-Villalba – German Cancer Research Center (DKFZ), Germany

Sarah Teichmann – Wellcome Sanger institute, UK

Kun Zhang – Department of Bioengineering, University of California, US

Schedule

Day

Time (CET)

Speaker

Title

Tuesday 3rd

Tuesday 3rd

Wednesday 4th


Wednesday 4th

Thursday 5th

Thursday 5th

Friday 6th

Friday 6th

3:00-4:00 pm

5:00-6:00 pm

3:00-4:00 pm


5:00-6:00 pm

1:00-2:00 pm

5:00-6:00 pm

3:00-4:00 pm

5:00-6:00 pm

Ana Martin Villalba

Sten Linnarsson

John Marioni


Ed Lein

Naomi Habib

Kenneth Harris

Sarah Teichmann

Kun Zhang

Profiling stem cell decision at the single cell level

Molecular Architecture of the Developing Mouse Brain

Using single-cell genomics to understand cell fate decisions during early mammalian development

Comparative approaches to understand human brain cellular diversity

The Alzheimer’s brain: from single cells to cellular communities

Classes and continua of CA1 GABAergic neurons

Cell Atlas Technologies & the Gastrointestinal Tract

Integrative single-cell RNA and chromatin analysis of human organs

General information

Sessions: lectures are 45 min long and followed by a 15 min. Q&A .

Questions: participants can ask questions throughout the whole talk, and after, by typing them in the Zoom Q&A system.

Registration is free: participants need to register to get access to the Zoom link for the Webinar. 

The maximum capacity of our webinars has been reached. Therefore registration is closed. The course is sold out.

Online lecture series
with the support of the Bordeaux School of Neuroscience

The online lecture series will be hosted by the Cajal Administration in partnership with the Bordeaux School of Neuroscience.

For additional information on this online lecture series, please email the Cajal Programme administration at info@cajal-training.org.

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.

Experimental Neuroscience Bootcamp

NeuroKits are hybrid courses that combine online lectures on advanced neuroscience topics with hands-on experiments by sending a kit containing the course material wherever you are.

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

Voight-Kampff

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

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

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)

Registration

Registration fee: 450€ 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: 450for one person and one course kit + 150€ per additional person (without the course kit)

Application closed on 26 July 2021

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

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.

Extracellular Electrophysiology Acquisition 0522

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

Faculty

Alexandra Leighton

Alex Leighton

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

Instructors

Aarón Cuevas López – Universitat Politècnica de València, ES

Joana Neto, FCT NOVA, PT

Jonathan P. Newman – MIT and Open Ephys, USA

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.

Applications are closed. The course will be held again. You can express your interest in the course and we will contact you once the application call is open again.

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