All posts by Catarina

Optogenetics, chemogenetics, and biosensors for neural circuit research

Course overview

Genetically encoded tools for neuroscience enable precise observation and manipulation of defined neural cell types, in behaving animals. This course provides both breadth and depth in the theoretical and practical application of these tools across a variety of classes including experimental designs, and with an emphasis on hands-on experience.

After completing this course, a student should expect to be knowledgeable about a wide range of molecular tools, have experience with multiplexed read/write experimental design, understand how to integrate optical hardware with rodent behavior, and appreciate nuances between 1-photon and 2 photon implementations. Interpretation and data analysis are integrated across the course.

Course directors

Weizmann Institute of Science, Israel

Bordeaux University, France

University of Texas, Austin, USA

Keynote Speakers

Camilla Bellone – Univ. of Geneva, Switzerland
Christina Kim – UC Davis, USA
Karl Deisseroth – Stanford University, USA
Mackenzie Mathis – EPFL, Switzerland
Marie Carlen – Karolinska Institute, Sweden
Michael Bruchas – Univ. of Washington, USA
Simon Wiegert – Univ. Heidelberg, Germany
Stephan Herlitze – Bochum University, Germany
Valentina Emiliani – Institut de la Vision, France
Cyril Herry – Bordeaux University, France
Yaniv Ziv – Weizmann Institute of Science, Israel

Instructors

Daniel Jercog – Univ. of Copenhagen, Denmark
Eyal Bitton – Weizmann Institute of Science, Israel
Francois Blot – Institut de la Vision, France
Inbar Saraf-Sinik – Weizmann Institute of Science, Israel
Jesse Muir – UC Davis, USA
Jonas Wietek – Weizmann Institute of Science, Israel
Mario Carta – Univ. of Bordeaux, France
Meryl Malezieux – Max Planck Institute, Germany
Nikolas Karalis – Paris Brain Institute, France
Olivia Masseck – Univ. of Bremen, Germany
Pritish Patil – Weizmann Institute of Science, Israel
Quinn Lee – McGill University, Canada
Sean Piantadosi – Univ. of Washington, USA
Steeve Laquitaine – EPFL, Switzerland
Alon Rubin – Weizmann Institute of Science, Israel

Course content

The course will comprise keynote lectures, hands-on expert workshops in experimental sessions and data analysis. Keynote lecturers will provide an introduction to their respective fields and exciting recent findings, while expert workshops will be given by a selected set of instructors. Instructors will work with the students prior to the course to design and plan their experiments in detail.

Each student will have an opportunity to present his/her work in a poster session, and an interactive journal club will provide the students with an opportunity to present and discuss the seminal studies that have shaped modern neuroscience through the introduction of novel techniques. Following the success of a pilot session held in the previous course, we will also hold semi-formal discussions with directors and instructors about career development, scientific “soft skills” and science communication.

Techniques

Stereotaxic surgery: viral vector injection, fiberoptic implants, cranial windows
Wide-field fluorescence imaging in vivo
Two-photon fluorescence imaging in vivo
Optogenetic manipulations: somatic and presynaptic excitation/inhibition
Building and implanting electrode arrays for in-vivo recordings
In-vivo electrophysiological recordings
Spike sorting and electrophysiological data analysis
In-vitro imaging in cell culture
Fiber photometry recordings in behaving mice
Design and execution of behavioral experiments
Using DeepLabCut for behavioral analysis

Projects

● Imaging neural activity with open-source miniscopes

● Photo-pharmacological and wireless optogenetic tools

● Thalamocortical processing of memory

● Methods for the development and characterization of genetically encoded biosensors

● Miniscope calcium imaging and analysis of the spatial code in CA1

● Comparing fluorescence-based sensors for dendritic imagining with in vivo 2-photon microscopy

● Activity-based tagging of neurons for functional dissection experiments

● 2-photon fibreoscope for imaging and holographic optogenetics in freely moving animals

● Computational analytical methods to link high-dimensional neuronal population and behavioral data

● Large-scale electrophysiological investigation of circuit dynamics

● Optogenetic silencing of synaptic terminals in freely moving mice

● Analysis of high dimensional neuronal data

(Illumination and equipment for in-vivo set-ups provided by Prizmatix)

Class of 2024

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)

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.

Quantitative Approaches to Behaviour and Virtual Reality

Course overview

Quantitative studies of behaviour are fundamental in our effort to understand brain function and malfunction. Recently, the techniques for studying behaviour, along with those for monitoring and manipulating neural activity, have progressed rapidly. Therefore, we are organizing a summer course to provide promising young scientists with a comprehensive introduction to state-of-the-art techniques in quantitative behavioural methods.

This course’s content is complementary to other summer courses that focus on measuring and manipulation neurophysiological processes. Our focus is on methodologies to acquire rich data representations of behavior, dissect them statistically, model their dynamics, and integrate behavioral measurements with other kinds of neurobiological data. To this end, students will 1) fabricate devices for recording the behavior of experimental organisms (including flies, fish, and humans), 2) learn, under the guidance of the scientists developing these methods, the modern tools to analyze behavioral data from these organisms, and 3) in a week-long independent project develop and conduct a behavioral study of their own design, with the support and guidance of the course instructors and teaching assistants.

Course directors

Harvard University, USA

Northwestern University, USA

Imperial College London, UK

Champalimaud Research, Portugal

Keynote speakers

Ahmed Al-Hady (Max Planck Institute, Konstanz, Germany)
Kristin Branson (Janelia, USA)
Andre Brown (Imperial College, UK)
Bing Brunton (U Washington, USA)
Serena Ding (Max Planck Institute, Konstanz, Germany)
Gonzalo de Polavieja (Champalimaud, Portugal)
Kim Hoke (Colorado State University, USA)
Karla Kaun (Brown University, USA)
Kate Laskowski (UC Davis, USA)
Zach Mainen (Champalimaud, Portugal)
Talmo Pereira (Salk Institute, USA)
Nachum Ulanovsky (Weizmann Institute, Israel)
James Cotton (Northwestern, USA)
Juan Gallego (Imperial College, UK)
Greg Stephens (Vrije Universiteit Amsterdam)
Sama Ahmed (U Washington, USA)

Course content

This 3-week course is a practical “hands-on” introduction to advanced methods in behavioural tracking and analysis. Our educational goal is to cover sufficient background such that all participants will be able to establish these techniques in their home laboratories.

In the pedagogical portion of the course (blocks 1 and 2, see below) we will use two main experimental model systems: flies (Drosophila melanogaster), fish (Danio rerio), and humans (Homo sapiens). Several days of instruction will focus on the analysis of video, audio, and biosignal recordings. On these days, students will perform analyses on data from flies, fish, and humans which they acquired, videos we provide rodents behaving, or data from their own organism of choice. In the student project portion of the course (block 3), students may develop their experiments and analyses using organisms in use at the Champalimaud (subject to their availability) in addition to our main three model systems (flies, fish, and humans).

We will cover data acquisition (software, hardware, tools), preprocessing (single animal, body parts, and multiple animals tracking systems), data analysis (clustering, ethograms) and modeling.

Course format

The course is organized in 3 blocks. During the first block, the students will use fruit flies and humans as model organisms to learn, through hands-on device fabrication, environment design, and data acquisition, how modern ethological technology (e.g. video tracking, virtual reality, automation, optogenetics, etc.) can be used for quantitative behavioral experiments.

In the second block, students will zoom into their favourite species and learn and apply quantitative analysis methods (unsupervised and supervised ethograms, manifold inference, deep neural networks, theoretical modeling, etc.) to tackle questions about behavior and brain function.

In the third block, students will form small groups and deploy these new skills to design and implement a week-long research project of their choice that consolidates this new knowledge, culminating in presentations of their findings. The extended project will offer an opportunity for the participants to undertake novel state-of-the-art research supervised by international experts in the field.

In addition:

International speakers will give daily seminars to describe how quantitative tools of behavioural analysis have impacted their work. Several of these speakers will also conduct pedagogical sessions to instruct students in the devices and analyses they have developed. Students will have structured opportunities to interact scientifically and socially with course speakers outside of the lab.
Students will give daily micro-presentations on their successes and failures implementing the instructed techniques of blocks 1 and 2.
Students will give presentations, throughout the course, on the research they are pursuing in their home labs.
At the end of block 3, students will present their independent projects in a culminating research symposium.

Champalimaud Centre for the Unknown, Portugal

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

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

Registration

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

Applications now open.

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.

This 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

Champalimaud Research, Portugal

University of Pennsylvania, USA

University of Chicago, USA

Technical University of Munich, Germany

Keynote Speakers

Rafal Bogacz (Oxford, UK)
Alex Cayco-Gajic (Ecole Normale Superieure Paris, France)
Christine Constantinople (NYU, USA)
Rosa Cossart* (INSERM, Marseille, France)
Adrienne Fairhall (U Washington, USA)
Ken Harris* (UCL, UK)
Gilles Laurent (Max Planck Institute Frankfurt, Germany)
Ashok Litwin-Kumar (Columbia, USA)
Christian Machens (Champalimaud, Portugal)
Jakob Macke (University of Tubingen, Germany)
Srdjan Ostojic (Ecole Normale Superieure Paris, France)
Agostina Palmigiano (UCL, UK)
Joe Paton (Champalimaud, Portugal)
Vanessa Ruta* (Rockefeller University, USA)
Cristina Savin (NYU, USA)
Nate Sawtell (Columbia, USA)
Tim Vogels (IST, Austria)
Omri Barak (Technion, Israel)
Marion Silies (Johannes Gutenberg University, Germany)

(*) to be confirmed

Course content

This course is designed for graduate students and postdoctoral fellows from a variety of disciplines, including neuroscience, physics, electrical engineering, computer science, mathematics and psychology. Students are expected to have a keen interest and basic background in neurobiology, a solid foundation in mathematics, as well as some computing experience. A four-day pre-school in mathematics and programming is offered for students that want to catch up on their math and programming skills.

A maximum of 24 students will be accepted. Students of any nationality can apply. We specifically encourage applications from researchers who work in the developing world. All students will be selected according to the normal submission procedure. Applications will be assessed by a selection committee, based on the following criteria: the scientific quality of the candidate (CV), evidence that the course will afford substantial benefit to the candidate (motivation letter), and the recommendation letters.

Preliminary programme

All days are structured with a lecture during the morning (9 AM-12 PM), and more experimental learning & tutorials during the afternoon 2PM-7PM, followed by discussion.

Week 1

15 - 19 July

Introduction and Single Neuron Dynamics
Network Dynamics
Statistical models of neural data
Multivariate neuronal data analysis
Normative models

Week 2

22 - 26 July

Low dimensional network dynamics
Vision and cognition in drosophila
Unconventional model systems
Population coding and learning
Cortical circuits in vision and audition

Week 3

29 July - 2 August

Neural Reinforcement learning
Decision-making and control
Recurrent neural networks and probabilistic computation

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

Champalimaud Centre for the Unknown, Portugal

Registration

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

Applications closed.

Course overview

Progress in microscopy has a long history of triggering major advances in neuroscience, and it is accelerating on many fronts: morphological and functional labeling, microscope instrumentation and imaging modalities, image processing and data analysis etc. These innovations are potentiating our ability to monitor, measure and manipulate biological structures and activities inside complex and intact nervous system model systems with ever higher throughput, robustness, precision and sensitivity and on ever wider temporal and spatial scales.

This Cajal course will bring together leading developers and practitioners of cutting-edge imaging techniques that push the frontiers of neuroscience research. The course follows up on previous Cajal school editions on this topic. The course will cover a broad spectrum of concepts and practical techniques, both classic and new, to provide a solid basis and critical guidance for newcomers and experienced users alike, wishing to pick up skills and learn about new developments and avenues in microscopy and its impact on neuroscience.

The applications will span a wide spectrum of neurobiological topics and preparations in an exemplary fashion, from brain development, plasticity and neuro-immune system interactions in cell cultures, brain slices and in vivo using the mouse and zebrafish brain as main model systems.

A series of pedagogical lectures and seminars will be complemented by hands-on practical training in small groups using experimental setups and tools provided by the Bordeaux School of Neuroscience, the Bordeaux Imaging Center, the course faculty & instructors, including a number of leading research labs on Bordeaux Neurocampus, as well as brand-new demo equipment from microscope manufacturers.

Course directors

University of Bordeaux, France

University of Göttingen, Germany

Keynote speakers

Alexander Flügel – University of Göttingen, Germany
Anna-Sophia Wahl – University of Munich (LMU), Munich, Germany
Claire Wyart – Institut du Cerveau, Paris
Dmitri Rusakov – UCL, UK
Florian Engert – Harvard, USA
Johann Danzl – ISTA, Klosterneuburg, Austria
Jinny Kim – KIST, Seoul, South Korea
Laurent Groc – IINS, Bordeaux
Moritz Helmstaedter – MPI Brain Research, Frankfurt

Instructors

Brugiere Thibault, Bordeaux, France

Agudelo Nathalie, ISTA, Austria

Ducros Matthieu, Bordeaux, France

Franz Jonas , Göttingen, Germany

Gaikwad Pranay , Bordeaux, France

Girard Jordan , Jordan Girard

Gockel Nala , Bonn, Germany

Haberl Michael, Göttingen, Germany

Kim Jihyun, Korea

Merlini Arianna , Göttingen, Germany

Mittag Manuel, Bonn, Germany

Müller Gesine, Göttingen, Germany

Offner Thomas, Göttingen, Germany

Okuda Kosuke, Bordeaux, France

Tonnesen Jan, Bilbao, Sapin

Würfel Thea, Göttingen, Germany

Ytavakoli Mojtaba, ISTA, Austria

Yulia Dembitskaya, Bordeaux, France

Course content

Course Format and Topics

Overall, the program is split into these broad complementary categories:

Multi-scale imaging of fixed brain tissue: from EM and super-resolution imaging to cleared tissue imaging
From in vitro to in vivo imaging in brain preparations
Functional neuronal imaging in behaving organisms

The course is divided into two 9-day long experimental blocks, offering each 6 to 8 experimental projects, where teams of 2 to 3 students pick projects for both blocks based on interest and compatibility.

The main goals of the course are to:

Teach students the theoretical foundation of advanced imaging techniques for molecular, cellular and systems neuroscience research.
Enable them to design and carry out frontier imaging experiments, analyze the results and present them to the other students and faculty at the end.
Allow them to gain enough relevant experience and build a knowledge base & network (with peers, faculty and companies) about the approaches to be able to establish them in their labs upon return.

Projects

This course offers experimental projects in these concrete areas:

Nanoscale monitoring and manipulation of the dynamic molecular organization of synapses using STED, SMLM and EM approaches.
Functional imaging of neuronal and astroglial cellular and network activity using modern optical biosensors for calcium (intra- and extracellular), synaptic glutamate, dopamine and other signaling molecules.
Shadow imaging of anatomical micro-structures and spaces in brain slices and in vivo using a variety of imaging modalities, including STED, confocal, 2-photon and light sheet microscopy in wildtype and animal models of brain diseases.
Super-resolution imaging of the biophysical properties (viscosity, topology) of the extracellular space using single-particle tracking (QD and carbon nanotubes).
Whole-brain multi-scale imaging by tissue clearing, expansion microscopy, and light sheet microscopy
Fast functional imaging in behaving zebrafish, danionella and other emerging model organisms
Imaging and analysis of chemotactic leukocyte migration in 3D environments
Functional imaging of calcium imaging in immune cells in vitro and in vivo.
Intravital Imaging via two-photon microscopy of immune cell motility in the CNS in healthy and autoimmune conditions

Bordeaux School of Neuroscience, France

Registration

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

Applications closed on 3 July 2024

The Brain Prize Course: Movement and motor control in health and disease

Course overview

The ability to move in an automatic or a goal-directed manner is a crucial function for many living organisms to survive and interact efficiently with their environments. Movements generation depend on the coordinated activity of motor centres that are distributed in the cortex, the basal ganglia, the cerebellum, and the brainstem but that, altogether, shape the descending motor commands sent to the spinal cord which will then execute the appropriate movements by controlling the activity of motoneurons. Any alteration in these systems and/or their interaction will impair the flow of information leading to disastrous motor disorders. In this CAJAL course, we will not only discuss the common organization of motor centres across species (from lamprey to primate) but also the neuronal mechanism and dynamics that underlie spontaneous and voluntary movements as well as how pathological alteration of these activities can lead to detrimental motor performances and disease state.

The goal of this CAJAL course is to instruct promising young neuroscientists to the advanced scientific concepts established in the field of motor control. We will present the latest discoveries that has been made in different species that shed light on how voluntary and goal-directed movements are generated. We will also describe the computational advances and analysis method that has pushed the limit of understanding movement generation.

Partner

Course directors

University of Copenhagen, Denmark

Paris Brain Institute, France

University of Bordeaux, France

Seminal Lecture

Réjean Dubuc – Université de Montréal, Canada

Honorary lectures from Brain Prize Winners

Silvia Arber – Basel University, Switzerland
Ole Kiehn – University of Copenhagen, Denmark

Keynote Speakers

David McLean – Northwestern University, USA
Lora Sweeney – Institute of Science and Technology A., Austria
Jonathan Whitlock – KISN, Norway
Camille Jeunet – INCIA CNRS, Bordeaux University, France
Marie-Laure Welter – Paris Brain Institute, France
Joaquim Alves da Silva – Champalimaud CU, Portugal
Gilad Silberberg – Karolinska Institutet, Sweden
Claire Meehan – University of Copenhagen, Denmark
Ian Duguid – University of Edinburgh, UK
Samuel Sober, Emory University, USA

Instructors

Amanda Jacob, Emory University, USA
Arthur Leblois, University of Bordeaux, France
Brice De la Crompte, Université de Bordeaux, France
Carmen Guerrero Marquez, University of Bordeaux, France
Constantinos Eleftheriou, University of Edinburgh
Emeline Pierrieau, University of Bordeaux, France
Filipa Barros, Champalimaud Centre for the Unknown, Portugal
Florina Toma, Institute of Science and Technology A., Austria
Graziana Gato, University Hospital Cologne
Joshua Dacre, University of Edinburgh
Kevin Fidelin, Paris Brain Institute, France
Kristen Frenzel, Emory University, USA
Lise Guilhemsang, University of Bordeaux, France
Marc Deffains, University of Bordeaux, France
Marco Romanato, Paris Brain Institute, France
Matthias Gruhn, University Hospital Cologne
Roberto De la Torre, Karolinska Institutet, Sweden
Salif Komi, University of Copenhagen, Denmark
Xinyu Jia, Paris Brain Institute, France

Course content

The course will feature a series of honorary lectures by two of the 2022 Brain Prize winners, keynote lectures, and hands-on expert workshops covering experimental sessions and data analysis. Keynote lecturers will introduce their respective fields and share their latest exciting discoveries. Expert workshops, led by a select group of instructors, will provide in-depth, practical training.

Participants will receive hands-on training on state-of-the-art methods applied to the study of motor control in the field including motor tracking, optogenetics manipulation, calcium imaging, high-density electrophysiology recording and data analysis. Prior to the course, instructors will work closely with students to design and plan the detailed experiments conducted during the miniproject, ensuring a tailored and enriching learning experience. Each student will have the opportunity to present their research through short communications and a poster session. Additionally, students will showcase the results of their miniprojects conducted during the workshop.

Throughout the course, students will have numerous opportunities to build their scientific network and engage with course directors, keynote speakers, instructors, and peers.

The course will be an intensive 3-week theoretical and practical course with two main goals:

1) Teaching students the theoretical foundation of the techniques (in week 1 and 2).

2) Give them enough hands-on experience to create an experimental mini-project (week 1) that will be carried out (in weeks 2 and 3) so they can establish these methods when they get back to their labs.

Techniques

– Stereotaxic surgery: viral vector injection, cranial windows, fiber optic, and miniscope implantation.

– In vivo one-color and dual-color calcium imaging

– High-density in vivo electrophysiological recordings using Neuropixel probes

– Ex vivo and in vivo patch clamp recordings

– Building a brain-computer interface to decode movement

– Muscle fibers recordings using high-density Myomatrix arrays

– Using open-source tools to build motor behavioral apparatus

– In vivo optogenetic manipulations during motor behavior

– Motor behavior in zebrafish larva and rodents

– Modelling the motor system & Data analysis

Projects

Hands-on projects will include:

Simultaneous imaging of D1 and D2 medium spiny neurons’ activity in freely moving mice.
Investigating connectivity among reticulospinal neurons in vivo.
Estimating how many reticulospinal neurons are sufficient to trigger locomotor bouts.
Understanding locomotion behaviour in Parkinson’s disease through quantitative measures – From lab to real world.
Investigating the motor functions of diverse classes of hindbrain and spinal interneurons via CRISPR/Cas genome editing in Xenopus.
Ex vivo and in vivo patch clamp recordings.
Neuropixel recording in mice performing a Forelimb Reaching task
Modeling the motor system.
Advancing Neuroscience Research with Myomatrix Arrays: High-Resolution EMG Recordings in Freely Behaving Mice and Stick Insects
Using and developing open-source tools to investigate motor behavior and its neuronal correlates.
Build a basic brain-computer interface for decoding movement intention.
Activity of Globus Pallidus Arkypallidal neurons during skilled-reaching movements in mice.
Pathophysiology of bradykinetic motor behavior in a non-human primate model of Parkinson’s disease.
Modelling the mouse spinal cord structure and its emergent dynamics in space.
Functional connectivity in the song-related basal ganglia-thalamo-cortical loop

Bordeaux School of Neuroscience, France

Registration

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

Visual Reactive Programming – Bonsai 1023

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

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

Course overview

Course directors

Keynote Speakers

Instructors

Course content

Techniques

Projects

Class of 2024

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote speakers

Course content

Course format

Champalimaud Centre for the Unknown, Portugal

Registration

Course overview

Course directors

Keynote Speakers

Course content

Preliminary programme

Week 1

15 - 19 July

Week 2

22 - 26 July

Week 3

29 July - 2 August

Champalimaud Centre for the Unknown, Portugal

Registration

Sponsors

Course overview

Course content

Course Format and Topics

Projects

This course offers experimental projects in these concrete areas:

Bordeaux School of Neuroscience, France

Registration

Course overview

Partner

Course directors

Seminal Lecture

Honorary lectures from Brain Prize Winners

Keynote Speakers

Instructors

Course content

Techniques

Projects

Hands-on projects will include:

Bordeaux School of Neuroscience, France

Registration

Course overview

Course Teaser

What will you learn?

Faculty

Gonçalo Lopes

Instructors

Course sponsors

Programme

Day 1 – Introduction to Bonsai

Day 2 – Cameras, tracking, controllers

Day 3 – Real-time closed-loop assays

Day 4 – Operant behavior tasks

Day 5 – Visual stimulation and beyond

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

Registration

Sponsors