All posts by Elena Dreosti

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

Single cell profiling and analysis in neuroscience

Course overview

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

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

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

Course partner

Course directors

Department of Medical Biochemistry and Biophysics,  Karolinska Institute,  Sweden

Biomedical Informatics, Harvard Medical School, USA

University of Cádiz/INiBICA, Spain

CNRS – IINS, University of Bordeaux, France

Keynote Speakers

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

Instructors

Marek Bartosovic – Karolinska Institutet (Sweden)
Lisa Bast – Karolinska Institutet (Sweden)
Pierre Boyeau – UC Berkeley (USA)
Hattie Chung – Broad Institute/MIT (USA)
Lisbeth Harder – Karolinska Institutet (Sweden)
Martin Häring – University Clinic Münster (Germany)
Hannah-Sophie Hochgerner – Technion (Israel)
Sergey Isaev – Moscow Institute of Physics and Technologies (Russia)
Danny Kitsberg – Jerusalem University (Israel)
Gioele La Manno – EPFL (Switzerland)
Christoffer Langseth – Stockholm University (Sweden)
Christian Mayer – Max Plank Institute (Germany)
Viktor Petukhov – University of Copenhagen (Denmark)
Anna Schaar – Helmholtz Zentrum München (Germany)
Milda Valiukonyte – Karolinska Institutet (Sweden)
Zinah Wassouf – Wellcome Sanger Institute (UK)

Course content

Topics & Techniques

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

The course will cover following topics:

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

Projects

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

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

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

– Project 3: GABAergic neuronal diversity across different forebrain structures

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

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

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

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

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

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

– Project 10: InCiteSeq

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

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications closed on 21st February 2022

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

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

Course sponsors

Interacting with neural circuits

Course overview

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

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

Course directors

Michael Hausser

Course Director

Wolfson Institute for Biomedical Research, UCL, UK

Claire Wyart

Course Director

Paris Brain Institute, ICM, France

Tiago Branco

Course Director

Sainsbury Wellcome Centre, UK

Susana Lima

Course Director

Champalimaud Foundation, Portugal

Keynote Speakers

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

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

Instructors

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

Course content

Schedule

Week 1

Sunday, June 19th: Arrival & Welcome reception
Monday, June 20th: Keynote lecture by Chris Xu / Ed Boyden Afternoon: Student presentations & Poster session I
Tuesday, June 21st: Keynote lecture by Eugenia Chiappe / Pavan Ramdya Afternoon: TA & Experimental Resources presentation & Poster session II
Wednesday, June 22nd: Keynote lecture by Greg Jefferis / Tiago Branco Afternoon TA & Experimental Resources presentation / Project Design & Discussion
Thursday, June 23rd: Morning tutorial by Scott Waddell / Na Ji Afternoon: Rig rotation / Project Design & Discussion
Friday, June 24th: Keynote lecture by Winfried Denk / Susana Lima Afternoon: Rig rotation/ Project Design & Discussion
Friday, June 25th: Surf/Beach Day

Week 2

Sunday, June 26th: Keynote lecture by Darcy Peterka / Nick Steinmetz / Botond Roska Afternoon: Rig rotation
Monday, June 27th: Keynote Lecture by Marius Pachitariu / Carsen Stringer Afternoon: Miniprojects
Tuesday, June 28th: Keynote lecture by Karel Svoboda / Ana João Rodrigues Afternoon: Miniprojects
Wednesday, June 29th: Keynote lecture by Isaac Bianco Afternoon: Miniprojects
Thursday, June 30th: Keynote lecture by Michael Brecht / Marta Moita Afternoon: Miniprojects
Friday, July 1st: Keynote lecture by Megan Carey Afternoon: Miniprojects
Saturday July 2nd: Keynote lecture by Francois St. Pierre / Michael Hausser / Afternoon: Free/Social

Week 3

Sunday July 3rd: Keynote lecture by Emily Dennis / Claire Wyart / Valentina Emiliani / Afternoon: Miniprojects
Monday, July 4th: Keynote lecture by Ofer Yizhar/ Afternoon: Miniprojects
Tuesday, July 5th: Keynote lecture by Michael Orger / Afternoon: Miniprojects
Wednesday, July 6th: Keynote lecture by Ken Harris / Afternoon: Miniprojects
Thursday, July 7th: Keynote lecture by Mackenzie Mathis Afternoon: Miniprojects
Friday, July 8th: Miniproject presentation
Saturday, July 9th: Departure

Topics & Techniques

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

Zebrafish

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

Mice

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

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

Champalimaud Centre for the Unknown, Portugal

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

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

Registration

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

Application closed on 24th January 2022

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

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

Sponsors

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

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

Computational Neuroscience

Course overview

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

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

Course directors

Brent Doiron

Course Director

University of Chicago, USA

Geffen

Maria Geffen

Course Director

University of Pennsylvania, USA

Gjorgjieva

Julijana Gjorgjieva

Course Director

Max Planck Institute for Brain

Research, Germany

Joe Paton

Course Director

Champalimaud Foundation, Portugal

Keynote Speakers

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

Instructors

Dylan Festa – Max Planck Institute for Brain Research, Germany
Francesca Mastrogiuseppe – Champalimaud Foundation, Portugal
Carlos Stein – Champalimaud Foundation, Portugal
Janaki ShethUniversity of Pennsylvania, USA
Alex Cayco-Gajic – École Normale Supérieure, France

Course content

Projects

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

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

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

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

Project 5. Finding structure in natural behavior (Murthy)

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

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

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

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

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

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

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

Preliminary programme

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

Week 1

17-22 July

  • Arrival and Welcome reception

  • Introduction and Single-Neuron Dynamics

  • Statistical analysis of neural data

  • Network dynamics

  • Normative models

  • Physical Constraints on Computing

23-24 July

Social event and free time

Week 2

25-29 July

  • Sensory coding and receptive fields

  • Spatial coding and memory

  • Vision

  • Neural Circuits and Synaptic Plasticity

  • Map formation and self-organization

30-31 July

Social event and free time

Week 3

1-5 August

  • Balanced Networks & Efficient Population Coding

  • Dendritic Computations & Birdsong Production

  • Reinforcement learning

  • Project work and presentations

6 August

Departure

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

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

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

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

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

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

Self-evaluation:

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

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

Champalimaud Centre for the Unknown, Portugal

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

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

Registration

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

Pre-school fee: 500 €

Applications closed on 28th March 2022

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

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

Visual Reactive Programming – Bonsai 1022

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 second edition. 

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.

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€ for any additional person (without the course kit)

Applications are closed. However you can express your interest in this NeuroKit course*
and we will contact you once the application call for the next edition is open.

You can also register to the Cajal newsletter at the bottom of this page.

*Please note that this is not considered as a valid application.

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