All posts by Elena Dreosti

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

Technical University of Munich, 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
Ann Kennedy, Northwestern University, USA

Instructors

Dylan Festa – Technical University of Munich, Germany
Francesca Mastrogiuseppe – Champalimaud Foundation, Portugal
Carlos Stein – Champalimaud Foundation, Portugal
Janaki ShethUniversity of Pennsylvania, USA

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.

Sponsors

Supported by a gift from the Simons Foundation

Visual Reactive Programming – Bonsai 1022

Applications are closed but you can express your interest in the next edition by clicking on the button above and filling in the form.

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

Researchers can participate from anywhere in the world because the course material is shipped to participants in a kit box that contains all the tools needed to follow the online course.

This course is now at its third edition. It is held at least once a year.

Call for TAs: If you already know how to programme in Bonsai and you would like to run this course locally as a Teaching Assistant with a group of students, please click on the button below to fill in the TA form. Thank you.

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 – NeuroGEARS, London, UK

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 13:00 to 17:00 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).

The CAJAL programme can offer some stipends (waived partial or full registration fee). Please apply through the course online application form.

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 but you can express your interest in the next edition by clicking on the button above and filling in the form.

Please note that this is not considered as an application.

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

Sponsors

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.

Pre-course for TAs

We are running a pre-course in early November at the EPFL in Geneva (Switzerland) and online, on November 7 – 11, 2022, to train Teaching Assistants. If you would like to help us teach this course locally or online, you can email us at info@cajal-training.org

Faculty

Alexander Mathis

Course Director EPFL, Switzerland

Danbee Kim

Co-director NeuroGEARS, UK

Keynote speakers

Nicola Clayton (Cambridge University, UK)

Ole Kiehn (Copenhagen University, Denmark)

Guest lecturers

Johanna T Schultz (USC, Australia)

Caleb Weinberg (Harvard Medical School, USA)

Nacho Sanguinetti (Harvard University, USA)

Local training hubs:

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

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).

Applications closed on 24 October 2022, 23:59 CEST

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

Optogenetics, chemogenetics and biosensors for cellular and circuit neuroscience

Course overview

Spatio-temporally precise manipulation and read-out of brain circuit function has been one of the longest-standing challenges in neuroscience. The recent explosion in the field of genetically encoded tools to control and measure neuronal activity has greatly facilitated investigation of brain function, ranging from single synapses to large-scale circuits. Both control and readout of neuronal activity can now be achieved over orders of magnitude in space and time, ranging from micrometers to entire brain regions and from milliseconds to days.

This course will provide participants with the opportunity to gain hands-on experience using the latest genetically encoded tools and state-of-the-art equipment for brain circuit investigation. A particular focus will lie on multiplexed manipulations and read-out of brain circuits. Participants will be familiarized with the biophysical principles behind the sensors and actuators, and given training complementary to their background in the technical aspects of experimental approaches.

Hands-on experiments will employ optogenetic and chemogenetic actuators, including excitatory and inhibitory ion channels, pumps, enzymes and G-protein coupled receptors. These actuators will be complemented by genetically encoded indicators of neural activity, including calcium and voltage indicators as well as indicators for neurotransmitters and neuromodulators such as glutamate, dopamine and norepinephrine.

The course will cover a wide range of experimental systems with an emphasis on functional brain circuits in vivo. Finally, participants will be guided through data analysis and conceptual interpretations of their experiments.

Course partner

Course directors

Ofer Yizhar

Course Director

Weizmann Institute of Science

Israel

Michael Lin

Co-director

Stanford University

USA

Simon Wiegert

Co-Director

Center for Molecular Neurobiology Hamburg (ZMNH)

Germany

Anna Beyeler

Co-director

University of Bordeaux

France

Keynote speakers

Adam Cohen – Harvard University, USA
Stephane Dieudonne – University of Marseille, France
Valentina Emiliani – Institut de la vision, France
Stefan Herlitze – University of Bochum, Germany
Na Ji – University of Berkeley, USA
Tom Kash – University of North Carolina, USA
Tatiana Korotkova – MPI Köln, Germany
Adam Packer – University of Oxford, UK
Tommaso Patriarchi – ETH Zurich, Switzerland
Jonas Wietek – Weizmann Institute of science, Israel
Yaniv Ziv – Weizmann Institute of science, Israel

Instructors

Yoann Atlas – Institut de la vision, France
Imane Bendifallah – Institut de la vision, France
Miklos Boldogkoi – Institute of Molecular and Clinical Ophthalmology Basel IOB, Switzerland
Martina De Gennaro – Institute of Molecular and Clinical Ophthalmology Basel IOB, Switzerland
Alexander Dieter – Center for Molecular Neurobiology Hamburg – ZMNH, Germany
Andrey Formozov – Center for Molecular Neurobiology Hamburg ZMNH, Germany
Nitzan Geva – Weizmann Institute of science, Israel
Christianne Grimm – Institut de la vision, France
J. Quinn Lee – McGill University, Canada
Maxime Maheu – University Medical Center Hamburg-Eppendorf, Germany
Mathias Mahn – Friedrich Miescher Institute of Basel, Switzerland
Vasyl Mykytiuk – Max Plank Institute, Germany
Praneeth Namburi – Massachusetts Institute of Technology, USA
Mauro Pulin – Center for Molecular Neurobiology Hamburg – ZMNH, Germany
Inbar Saraf-Sinik – Weizmann Institute of science, Israel
Robson Scheffer Teixeira – University of Cologne, Germany
Guilherme Silva – University of Harvard, USA
Dimitrii Tanese – Institut de la vision, France

Course content

Topics & Techniques

The following techniques will be covered during the course:

  • implantation of optical fibers, stereotactic injection of viruses in mice.
  • optogenetic stimulation (BIPOLES) and monitoring of pupil size and mouse behavior.
  • imaging of calcium responses, building of a reward delivery system and a head-fixation system for mice either immobilized in a tube or running on a treadmill.
  • in vitro exploration of FLARE technique
  • 2-photon holographic illumination to achieve single-cell resolved optogenetic activation of presynaptic cells and patch-clamp recording of the post-synaptic neuron
  • concurrent photostimulation and calcium imaging of the presynaptic cells, and voltage imaging on the post-synaptic cell
  • use of miniature head-mounted microscopes (Inscopix).
  • perform population level data analysis on data that was collected across multiple days
  • behavioral assays including the elevated plus maze, the open field test, consumption of water, sucrose, quinine and food, as well as mild foot shocks
  • head-bar implantation, stereotaxic intracerebral virus injection, and craniotomy preparation for long-term recordings
  • head-fixed electrophysiology setup building
  • silicon-probe recordings, in head-fixed mice during behavior, using multi-shank, high-density silicon probes (128-512 channels) & Physiological monitoring
  • opto-tagging and optogenetic manipulations of specific cell-types.
  • open-source hardware and software for the acquisition and processing of the data, including OpenEphys, Bonsai, PulsePal, Cyclops, Arduino, Linux, KiloSort, and MountainSort
  • construct microdrives, mount the silicon probes onto them, make optical fibers of custom length

Projects

  • Project 1: “Optogenetic control of neuromodulation ”
  • Project 2: “Optical tool exploration in culture, in slice, and in vivo”
  • Project 3: “Optical tool exploration in culture, in slice, and in vivo”
  • Project 4: “Probing neuronal excitability with Arch-derived voltage sensors ”
  • Project 5: “Longitudinal calcium imaging in freely behaving mice using Inscopix system”
  • Project 6: “In vivo imaging of divergent neural populations using dual-color fiber photometry”
  • Project 7: “All optical characterization of eOPN3 mediated terminal inhibition in vivo”
  • Project 8: “Large-scale electrophysiology and optogenetics during head-fixed behavior”
  • Project 9: “In vivo calcium imaging with open-source Miniscopes”
  • Project 10: “Combining in vivo electrophysiology and optogenetics in freely moving mice”
  • Project 11: “All optical interrogation of dopamine circuits in freely moving mice using multiplexfiber photometry and biosensors”
  • Project 12: “All-optical manipulation and read-out of synaptic transmission”

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 7 December 2020

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.

COVID-19 update: In case the Optogenetics, chemogenetics and biosensors for cellular and circuit neuroscience course is postponed due to the pandemic, all applicants will have the choice to maintain their application or cancel it. Applicants who were already selected to attend will not have to reapply and will automatically be enrolled in the rescheduled course.
In addition, the Cajal Programme will not, as far as possible, request the registration fee from selected applicants until the course has been secured and confirmed. Nevertheless, should the course be cancelled before the course dates and the registration fees already collected, participants will be reimbursed.

Course sponsors

Neuroepigenetics: writing, reading and erasing the epigenome

Course overview

This course is a theoretical and practical training on the recently emerged field of neuroepigenetics. It will provide an overview of the current concepts and knowledge on the nature and functions of the epigenome in the nervous system, its modes of regulation and its link to brain health and disease. It will combine lectures and hands-on projects to learn about state-of-the-art approaches and methodologies to study how the epigenome is established and modulated by behaviour in rodents and invertebrates, what machinery is involved and what is its causal relationship to functions. It will include methods in behaviour, epigenetics, (epi)genome editing, molecular and cell biology, -omics and bioinformatics.

This course wishes to foster the development of neuroepigenetics as a key discipline in the neurosciences, and train and educate young researchers expected to contribute to the field in the near future. It is intended for PhD students and early career postdocs who wish to acquire good bases and broad knowledge of the field.

Course partner

Course directors

Karine Merienne

Course Director

CNRS – LNCA, University of Strasbourg, France

Angel Barco

Co-Director

Neurosciences Institute (UMH-CSIC), Spain

André Fischer

Co-Director

German Center for Neurodegenerative diseases (DZNE), Germany

Institute of Informatics, University of Warsaw, Poland

Keynote Speakers

Elisabeth Binder – Max Planck Institute of Psychiatry, Munich, Germany
Anne-Laurence Boutillier – LNCA, Strasbourg, France
Goncalo Castelo Branco – Karolinska Institute, Stockholm, Sweden
Johannes Gräff – EPFL, Lausanne, Switzerland
Elizabeth A Heller – Penn Epigenetics Institute, Philadelphia, USA
Denes Hnisz – Max Planck Institute for Molecular Genetics, Berlin, Germany
Aleksandra Pekowska – Dioscuri Center of Chromatin Biology and Epigenomics, Poland

Instructors

Rafael Alcala Vida – Instituto de Neurociencias UMH-CSIC, Spain
Mykhailo Batiuk – EPFL, Lausanne, Switzerland
Davide Coda – EPFL, Lausanne, Switzerland
Charles Decraene – LNCA, Strasbourg, France
Beatriz del Blanco Pablos – Instituto de Neurociencias UMH-CSIC, Spain
Aleksander Jankowski – Institute of informatics, Warsaw, Poland
Lalit Kaurani – DZNE, Göttingen, Germany
Marta Kullis – IDIBABS, Barcelona, Spain
Stéphanie Legras – IGBMC, Strasbourg, France
Jose Lopez Atalaya – Instituto de Neurociencias UMH-CSIC, Spain
Pierre-Eric Lutz – INCI, Strasbourg, France
Magdalena Machnicka – Institute of informatics, Warsaw, Poland
Marta Alaiz Noya – Instituto de Neurociencias UMH-CSIC, Spain
Isabel Paiva – LNCA, Strasbourg, France
Jose Sanchez-Mut – Instituto de Neurociencias UMH-CSIC, Spain
Sophie Schroeder – DZNE, Göttingen, Germany
Tanya Vavouri – Pujol Research Institute, Badalona, Spain

Course content

Topics & Techniques

State-of-the-art approaches to produce and analyze cell-type-specific epigenomic data in the brain in physiological and disease contexts will be taught, as well as approaches to manipulate the epigenome in brain cells.

  • ChIP seq
  • CUT & Tag seq
  • ATAC seq
  • Single nuclei DNA methylome (snmC-seq2)
  • Single nuclei RNA seq
  • Sample preparation for simultaneous RNAseq, WGBSseq and/or singe-nuclei ATAC-RNAseq (multiome)
  • Design, production and manipulation of epi-editing tools using viral constructs and CRISPR system, and analysis of transcriptional changes at targeted loci
  • Mouse brain subregion dissection, tissue sectioning
  • Fluorescently activated nuclear sorting (FANS) of neuronal and non-neuronal cell populations from mouse brain tissue
  • Isolation of glial cells (astrocytes) from mouse brain tissue using magnetic beads (MACS)
  • RNAscope
  • Confocal microscopy
  • Primary cultures of hippocampal neurons.

Projects

Project 1: Cell-type-specific epigenetic profiling using Fluorescence-Activated Nuclear Sorting (FANS) from brain tissue

Project 2: Astrocyte epigenome of mouse hippocampus

Project 3: Transcriptomic profiling of adult mouse brain tissue using 10X Genomics single-nuclei RNA-sequencing

Project 4: Cell type-specific detection of lncRNAs in the mouse brain using RNAscope and immunofluorescence

Project 5: Investigation of single cell DNA methylome landscape of cortical brain cells

Project 6: Cell-type and brain-region specific epigenetic manipulation in Alzheimer’s disease models

Project 7: CRISPR-dCas9 systems for targeted epigenetic repression

Project 8: Epigenome editing technology based on the CRISPR/dCas9 system.

Computational projects: State-of-the-art approaches for bioinformatic analysis and interpretation of the next generation sequencing (NGS) data obtained in the epigenomic experiments covered in the first block.

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 5th September 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 process, depending on the course.

Our partner, ERA-NET NEURON, will also offer grants to participants who are part of an ERA-NET Neuron research group. Please indicate in the application form if you are a member of the network.

Course sponsors

Thanks to Bordeaux University Platforms

Extracellular Electrophysiology Acquisition 1221

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

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 courses will be held from 14:00 to 18:00 GMT.

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

The applications closed on 18 October 2021.

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

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