Category Archives: 2023

Extracellular Electrophysiology Acquisition 1023

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

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

This course is now at its third edition.

Course overview

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

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

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

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

Course sponsors

What will you learn?

By the end of the course, you will:

  • be familiar with the electronic building blocks of acquisition systems

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

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

Course Directors

Cecilia Herbert

Course Director

Open Ephys Production Site, PT

Jakob Voigts

Course Director

MIT and Open Ephys, USA

Filipe Carvalho

Course co-director

Open Ephys Production Site, PT

Guest video lecturers

– Alex Leighton, Open Ephys Production Site, PT

– Joana Neto, FCT NOVA, PT

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

-Filipe Carvalho, Open Ephys Production Site, PT

Teaching Assistants

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

Course designers

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

Programme

Day 1 – Introduction

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

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

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

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

Day 2 – Impedance

  • Using microcontrollers to acquire physiological data.

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

  • Understanding the function and limitations of operational amplifiers.

Cajal Images -Day 1
Cajal- Day 3

Day 3 – Data Acquisition

  • Understanding Instrumentation Amplifiers.

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

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

Day 4 – Synchronizing Datastreams

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

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

  • Designing student projects and group feedback on plan.

Day 5 – Project and Open-Source Neuroscience

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

  • An overview of open-source community projects.

  • Student project presentation.

Cajal- Day 4

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

Registration

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

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

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

Connectomics from micro- to meso- and macro-scales

Course overview

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

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

Course directors

Gregory Jefferis

Course Director

MRC LMB and University of Cambridge, UK

Jinny Kim

Course Director

Korea Institute of Science and Technology, Korea

Nicolas Renier

Course Director

Paris Brain Institute, France

Allen Institute of Brain Science, US

Keynote Speakers

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

Instructors / Teaching Assistants

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

Course content

Light Microscopy and functional, molecular methods:

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

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

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

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

Electron microscopy synaptic connectomics:

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

Techniques

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

Projects

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

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications closed 17 April 2023

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

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

Advanced techniques for synapse biology

Course overview

Synapses are sites of information transfer and storage in the brain. These specialised structures integrate complex signals and undergo functional changes that underlie the formation of memories. Synaptic dysfunction is associated with early stages of neurodegenerative disorders such as Alzheimer’s disease, and underlies neurodevelopmental disorders such as autism spectrum disorders and intellectual disability.

Studying synapse function and plasticity is key to understanding brain circuits that underlie behaviour, and to identify synaptic malfunction mechanisms underpinning brain diseases. This course will allow students to integrate theoretical and methodological concepts on synapse biology with hands-on experience on state-of-the art imaging, functional and computational methodologies. The course provides an in-depth understanding to many concepts such as synapse formation and maintenance, pre- and postsynaptic mechanisms, structural and functional synaptic plasticity, synaptic integration in neuronal networks and synaptopathies. Hands-on experimental projects conducted in small groups with the support of senior scientists will expose the students to methodologies at the forefront of research in this field.

Course directors

Ana Luisa Carvalho

Course Director

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

Mathieu Letellier

Course Director

IINS, University of Bordeaux, France

Hey-Kyoung Lee

Course Director

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

Keynote Speakers

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

Instructors

Alexy Louis – IINS, Univ of Bordeaux, France

Anne-Claire Compagnion – Univ. Lausanne, Switzerland

Elena Baz-Badillo – IINS, Univ Bordeaux, France

Frederic Gambino – IINS, Univ Bordeaux, France

Joana Ferreira – CNC, Univ Coimbra, Portugal

Julia Bär – Humboldt Universität zu Berlin, Germany

Julien Dupuis – IINS, Univ Bordeaux, France

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

Léa Sarzynski – IINS, Univ Bordeaux, France

Lucille Alonso – IINS, Univ Bordeaux, France

Luís Ribeiro – CNC, Univ Coimbra, Portugal

Margaux Giraudet – IINS, Univ Bordeaux, France

Marie-Lise Jobin – IINS, Univ Bordeaux, France

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

Michelle BridiWest Virginia University, USA

Mónica Santos – CNC, Univ Coimbra, Portugal

Olivier Nicole – IINS, Univ Bordeaux, France

Tamara Buijs – Netherlands Institute for Neuroscience, Netherlands

Vivek Belapurkar – IINS, Univ Bordeaux, France

Course content

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

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

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

Topics

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

Course format

Three weeks of intensive training, with students in the lead, supported by senior scientists

The course includes both lectures by leading scientists in synapse biology, and hands-on training in two projects of about 9 days each, supported by senior scientists. Students (20 maximum) will attend theoretical and methodological lectures during the morning sessions, and spend the afternoon period in the Neuroscience Training Lab at the Neurocampus performing projects in groups of 2-3 students. The training laboratory is dedicated to the course and it is equipped with a wet lab for cellular and molecular biology, cell culture and animal rooms, electrophysiology rigs and behavior set-ups. Students will have access to core facilities at the University of Bordeaux, including to the Bordeaux Imaging Center, the Functional Genomics and the Biochemistry facilities. Support and expertise to carry out the projects is provided by external instructors coming from leading international laboratories in synapse biology, who will be present throughout the duration of the projects and assist students in their experiments (one instructor per group). Students are encouraged to participate in the design of projects, ahead of the course, through interaction with their project instructor. Students are welcome to bring their constructs or models, to be integrated in the project to be conducted. At the end of each project, students will present their findings and discuss with colleagues and instructors. Extracurricular activities (such as panel discussions on ethics, diversity and equity in Neuroscience), outreach activities and social events are also planned.

Techniques

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

Experimental projects:

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

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications closed 29 May 2023

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

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

Modern Approaches to Behavioural Analysis

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

Course overview

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

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

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

What will you learn?

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

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

By the end of the course, you will:

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

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

Faculty

Course directors

Alexander Mathis

Course Director EPFL, Switzerland

Danbee Kim

Matter Neuroscience, UK

Course contributors

Nicola Clayton, keynote lecture (Cambridge University, UK)

Ole Kiehn, keynote lecture (Copenhagen University, Denmark)

Johanna T Schultz, guest lecture (USC, Australia)

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

Nacho Sanguinetti, guest lecture (Harvard University, USA)

Local Training Hubs

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

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

1. Argentina, Buenos Aires

2. Germany, Bochum

3. Greece, Athens

4. Japan, Okinawa

5. Switzerland, Geneva

6. Rwanda, Kigali

7. United Kingdom, Oxford and London

8. Canada, Toronto

9. Germany, Bochum

10. Spain, Valencia

Apply to be a Teaching Assistant!

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

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

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

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

Here is our Global Reach in 2022 (past participants)

Programme

Day 1 – What is animal behaviour?

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

  • Practical exercises for training skills in observing and defining behaviours

Day 2 – Tools for modern-day ethology

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

  • Introduction to DeepLabCut

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

Day 3 – Training computers to see as we see

  • Multi-animal tracking

  • Live tracking

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

Day 4 – Analysis by eye and by computer

  • Movement kinematics in living biological systems

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

  • Analyse original video dataset of behaviour

  • Joint neural and behavioral analysis

Day 5 – Working on your data and discussion

  • Advanced DLC topics and potential pitfalls

  • Keep analyzing data and student presentations

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

Registration

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

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

Sponsors