Category Archives: 2021

Visual Reactive Programming – Bonsai 0121

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

Course overview

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

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

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

Course Teaser

What will you learn?

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

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

The online material will be soon found here.

Faculty

NeuroGEARS, London, UK

Instructors

João Frazão – Champalimaud Research, Lisbon, PT

Niccolò Bonacchi – International Brain Laboratory, Lisbon, PT

Nicholas Guilbeault – University of Toronto, CA

André Almeida – NeuroGEARS, London, UK

Bruno Cruz – Champalimaud Research, Lisbon, PT

Course sponsors

Programme

Day 1 – Introduction to Bonsai

Introduction to Bonsai. What is visual reactive programming.
How to measure almost anything with Bonsai (from quantities to bytes).
How to control almost anything with Bonsai (from bytes to effects).
How to measure/control multiple things at the same time with one computer.
Demos and applications: a whirlwind tour of Bonsai.

Day 2 – Cameras, tracking, controllers

Measuring behavior using a video.
Recording real-time video from multiple cameras.
Real-time tracking of colored objects, moving objects and contrasting objects.
Measuring behavior using voltages and Arduino.
Data synchronization. What frame did the light turn on?

Day 3 – Real-time closed-loop assays

What can we learn from closed-loop experiments?
Conditional effects. Triggering a stimulus based on video activity.
Continuous feedback. Modulate stimulus intensity with speed or distance.
Feedback stabilization. Record video centered around a moving object.
Measuring closed-loop latency.

Day 4 – Operant behavior tasks

Modeling trial sequences: states, events, and side-effects.
Driving state transitions with external inputs.
Choice, timeouts and conditional logic: the basic building blocks of reaction time, Go/No-Go and 2AFC tasks.
Combining real-time and non real-time logic for good measure.
Student project brainstorming

Day 5 – Visual stimulation and beyond

Interactive visual environments using BonVision.
Machine learning for markerless pose estimation using DeepLabCut.
Multi-animal tracking and body part feature extraction with BonZeb.
Student project presentation.
Where to next.

Registration

Fee : 300 € (includes lectures and kit)

Application closed on 20 December 2020.

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

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

Extracellular Electrophysiology Acquisition 0321

To apply to the second edition of this course please visit this webpage

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

Course overview

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

Open Ephys Production Site, PT

MIT and Open Ephys, USA

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.

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.

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

Registration

Fee : 400€ (includes lectures and kit)

Application closed on 22 February 2021.

To apply to the second edition of this course please visit this webpage

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

Ageing cognition

Course overview

The normal aging process is associated with reduced performance on cognitive tasks that require one to quickly process or transform information to make a decision, including measures of speed of processing, executive cognitive function, working and relational memories. Structural and functional alterations in the brain correlate with these age-related cognitive changes, such as loss of synapses, and dysfunction of neuronal networks. It is crucial to develop new approaches that consider the whole neuroanatomical, endocrine, immunological, vascular and cellular changes impacting on cognition.

This 3-week course will cover the fundamentals of cognitive aging -including inter-individual differences, cognitive and brain reserve and risk factors- and highlight the newest functional imaging methods to study human brain function. The Faculty will share the state-of-the-art molecular, optical, computational, electrophysiological, behavioral and epidemiological approaches available for studying the aging brain in diverse model systems.

Students will learn the potential and limitations of these methods, through practical experience in a combination of lectures addressing aging in both humans and animal models and hands-on-projects. They will acquire sufficient practical experience to model, design and interpret experiments and brainstorm on novel technologies and hypotheses to explore the aging of the brain using more integrative and creative approaches.

Course directors

Neurobiology of Ageing & Disease
iMM Lisboa
Portugal

The Rotman Research Institute, Baycrest
& University Toronto
Canada

Neurocentre Magendie
INSERM U 1215 – University of Bordeaux
France

Keynote Speakers

Hélène Amieva – Bordeaux population Health Center, France
Adam Antebi – Max Planck Institute for Biology of Ageing, Germany
Carol Barnes – University of Arizona, USA
Luc Buée – University of Lille, France
Gwenaëlle Catheline – INCIA, Bordeaux, France
Maria Llorens-Martin – Universidad Autonoma Madrid, Spain
Aline Marighetto – Neurocentre Magendie, Bordeaux, France
Lars Nyberg – Umeå University, Sweden
Laure Rondi-Reig – Sorbonne Université, Paris, France
Yaakov Stern – Columbia University, USA

Instructors

Claudia Almeida – CEDOC, UNL, Lisbon, Portugal
Nicolas Blin – Neurocentre Magendie, Bordeaux, France
Vanessa Charrier – Neurocentre Magendie, Bordeaux, France
Joana Coelho – IMM, Lisbon, Portugal
Miguel De la Flor Garcia – Universidad Autónoma de Madrid , Spain
Nicole Etchamendy – Neurocentre Magendie, Bordeaux, France
David Koss – University of New castle, UK
Nuno Morais – IMM, Lisbon, Portugal
Paula Pousinha – IPMC, Nice, France
Miguel Remondes – IMM, Lisbon, Portugal
Jenny Rieck – Baycrest & Univ. Toronto,
Azza Sellami – Neurocentre Magendie, Bordeaux, France
Jean Vincent – Sorbonne Université, Paris, France

Course content

Projects

The following projects are confirmed so far:

Project 1: Is lysosome dysfunction a mechanism of synapse aging?
Project 2: Physiological signatures of cognitive aging
Project 3: Recording neuronal activity on hippocampal slices from aged mice
Project 4: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in humans based on a virtual radial-maze task.
Project 7: Immunohistochemistry on brain tissue obtained from aged humans and rodents
Project 8: Unveiling the transcriptomic signatures of human brain ageing
Project 9: In vivo optogenetic to manipulate adult neurogenesis
Project 10: Inducing Neurons (iNs) from human fibroblasts to preserved the cellular synaptic ageing-signature
Project 11 and 12: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in mice on a radial-maze task.
Project 13 and 14: Quantification of cortical DNA damage in age-associated neurodegenerative diseases.

For more information on projects and techniques which will be taught at the course, download the projects list.

Bordeaux School of Neuroscience, France

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

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

Registration

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

Application closed on 21 June 2021

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

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

Experimental Neuroscience Bootcamp

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

Course overview

This course provides a fundamental foundation in the modern techniques of experimental neuroscience. It introduces the essentials of sensors, motor control, microcontrollers, programming, data analysis, and machine learning by guiding students through the “hands on” construction of an increasingly capable robot.

In parallel, related concepts in neuroscience are introduced as nature’s solution to the challenges students encounter while designing and building their own intelligent system.

Course Partners

Voight-Kampff

What will you learn?

The techniques of experimental neuroscience advance at an incredible pace. They incorporate developments from many different fields, requiring new researchers to acquire a broad range of skills and expertise (from building electronic hardware to designing optical systems to training deep neural networks). This overwhelming task encourages students to move quickly, but often by skipping over some essential underlying knowledge.

This course was designed to fill-in these knowledge gaps.

By building a robot, you will learn both how the individual technologies work and how to combine them together into a complete system. It is this broad-but-integrated understanding of modern technology that will help students of this course design novel state-of-the-art neuroscience experiments.

Course directors

Programme

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

Day 1 – Sensors and Motors

What will you learn?

You will learn the basics of analog and digital electronics by building circuits for sensing the environment and controlling movement. These circuits will be used to construct the foundation of your course robot; a Braitenberg Vehicle that uses simple “algorithms” to generate surprisingly complex behaviour.

Topics and Tasks:

Electronics (voltage, resistors, Ohm’s law): Build a voltage divider
Sensing (light-dependent resistors, thermistors): Build a light/temperature sensor
Movement (electro-magentism, DC motors, gears): Mount and spin your motors
Amplifying (transistors, op-amps): Build a light-controlled motor
Basic Behaviour: Build a Braitenberg Vehicle

Day 2: Microcontrollers and Programming

What will you learn?

You will learn how simple digital circuits (logic gates, memory registers, etc.) can be assembled into a (programmable) computer. You will then attach a microcontroller to your course robot, connect it to sensors and motors, and begin to write programs that extend your robot’s behavioural ability.

Topics and Tasks:

Logic and Memory: Build a logic circuit and a flip-flop
Processors: Setup a microcontroller and attach inputs and outputs
Programming: Program a microcontroller (control flow, timers, digital IO, analog IO)
Intermediate behaviour: Design a state machine to control your course robot

Day 3: Computers and Programming

What will you learn?

You will learn how a modern computer’s “operating system” (Linux) coordinates the execution of internal and external tasks, and how to communicate over a network (using WiFi). You will then use Python to write a “remote-control” system for your course robot by developing your own communication protocol between your robot’s linux computer and microcontroller.

Topics and Tasks:

Operating Systems: Setup a Linux computer (Raspberry Pi)
Networking: Remotely access a computer (SSH via WiFi)
Programming: Program a Linux computer (Python)
Advanced behaviour: Build a remote control robot

Day 4: (Machine) Vision

What will you learn?

You will learn how grayscale and color images emerge and how to work with them in a Python environment. By mounting a camera on your robot, you can live-stream the images to your computer. You will then use background subtraction and thresholding to program an image-based motion detector. You will use image moments to detect and follow a moving light source, and learn about “classical” face detection.

Topics and Tasks:

Images: Open, modify, and save images
Camera: Attach and stream a camera image
Image processing: Determine differences in images
Pattern recognition: Extract features from images

Day 5: (Machine) Learning

What will you learn?

You will learn about modern deep neural networks and how they are applied in image processing. You will extend the intelligence for your robot, by adding a neural accelerator to the robot. We will deploy a deep neural network for face detection and compare it to the “classical” face detector. Ultimately, you will create and train your own deep neural network that will allow your robot to identify it’s creator, you.

Topics and Tasks:

Inference: Implement a neural accelerator (Google Coral USB EdgeTPU)
Deployment: Deploy and run a deep neural network
Object detection: Finding faces using a deep neural network (Single Shot Detector)
Object classification: Train a deep neural network to identify one’s own face (TF/Keras)

Registration

Registration fee: 450€ per person (includes shipping of the course kit, pre-recorded and live lectures before and during the course, full attendance to the course, and course certificate).

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

Application closed on 26 July 2021

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

Advanced imaging techniques for cellular and systems neuroscience (rescheduled)

Course overview

Rapid advances in live imaging of targeted cellular morphologies and functions underpin the emerging revolution in our understanding of synapses, circuits, and behaviour. This Cajal course will assemble, as international faculty, leading experts in developing and exploiting cutting-edge imaging techniques that have been propelling such advances. How to combine genetically encoded fluorescence labelling with behavioural designs, micro-circuit monitoring, or single-molecule tracking, how to avoid pitfalls of having false-positive observations and inherent noise, how to best analyse your multi-dimensional data will be, among others, the recurrent subjects of the course. An intense programme of lectures and seminars will be combined with supervised, hands-on practical training modules and group assignments using experimental setups and tools provided by the world-leading research environment of the Bordeaux School of Neuroscience.

Course partner

Course directors

UCL Queen Square
Institute of Neurology
United Kingdom

Neuronal circuits and behaviour
MPI for Metabolism Research
Germany

CNRS, IINS UMR 5297
University of Bordeaux
France

Keynote speakers

Thomas Blanpied – University of Maryland School of Medicine, USA
Daniel Choquet – IINS, University of Bordeaux, France
Rosa Cossart – CNRS, Inserm – INMED, Aix-Marseille Université, France
Olga Garaschuk – University of Tuebingen, Germany
Laurent Groc – IINS, University of Bordeaux, France
Michael Hausser – University College London, UK
Christian Henneberger – University of Bonn, Germany
Christophe Leterrier – INP CNRS-AMU UMR 7051,
Aix-Marseille Université, France
Valentin Nagerl – University of Bordeaux, France
Tim Ryan – Weill Cornell Medical College, USA
Ilaria Testa – KTH Royal Institute of Technology, Sweden
Andrea Volterra – University of Lausanne, Switzerland
Kirill Volynski – University College London, UK

Instructors

Stephane Bancelin – University of Bordeaux, France
Francisco de los Santos – MPI Cologne, Germany
Yulia Dembitskaya – University of Bordeaux, France
Ani Jose – IINS, University of Bordeaux, France
Olga Kopach – University College London, UK
Philipe R. F. Mendonça – University College London, UK
Dragomir Milovanovic – Charité University Clinic, Berlin, Germany
Christian Hoffmann – Charité University Clinic, Berlin, Germany
Jakob Rentsch– Charité University Clinic, Berlin, Germany
Petr Unichenko – University College London, UK
Olga Tiurikova – University College London, UK
Hanna Van Den Munkhof – MPI Cologne, Germany
Kaiyu Zheng – University College London, UK
Olivier Nicole – IINS, University of Bordeaux, France
Julien Dupuis – IINS, University of Bordeaux, France
Xuesi Zhou – IINS, University of Bordeaux, France

Course content

Topics & Techniques

Students will learn:

– Super-resolved organisation of the synaptic cleft.

– Nanoscale monitoring and probing of NMDA receptors.

– Super-Resolution probing of the axonal initial segment.

– RESOLFT nanoscopy.

– Super-Resolution Imaging of Brain Nano-Structure In Vivo.

– Nanoscale imaging and manipulation of synapse function to study the brain.

– Monitoring molecular machinery of synaptic plasticity.

– Probing the molecular basis of synaptic transmission.

– Optical sensors for neurotransmitters.

– Multiplexed imaging of presynaptic function.

– Ca2+ regulation of synaptic vesicle fusion in central synapses.

– Optical monitoring of volume transmission.

– Studying astrocytes in synaptic function with 1D-to-3D two-photon Ca2+ imaging.

Projects

For more information on projects download the “Programme info”

Project 1: “Imaging prefrontal cortex neurons encoding social information”.
Project 2: “Imaging hippocampal place cells in freely moving animals”.
Project 3: “FRET imaging of NMDA receptor co-agonists dynamics”.
Project 4: “Assessing the mechanosensitive properties of the membrane periodic skeleton
(MPS) in neurons”.
Project 5: “RESOLFT nanoscopy to study the fast reorganization of dendritic spines”.
Project 6: “Single synapse imaging of glutamate release and pre-synaptic Ca2+ for study of
pre-synaptic receptor function and short-term synaptic plasticity”.
Project 7: “Quantitative intracellular calcium measurements using fluorescent lifetime
imaging microscopy”.
Project 8: “A viral strategy for targeting and manipulating principal neurons: probing the
glutamatergic synapse function at multi-synapse imaging approach”.
Project 9: “Probing of astroglial Ca2+ dynamics in organised brain tissue through
fluorescent intensity and lifetime measurements”.
Project 10: “Multicolor multiphoton imaging of single synaptic release sites in vivo”.
Project 11: “High spatial-temporal imaging of a heterogeneous population of synapses in
neuronal cultures using the iGluSnFR probe”.
Project 12: “Super-resolution shadow imaging in the mouse brain”.
Project 13: “Dual color single particle tracking to study membrane receptors dynamics”.
Project 14: “Imaging tripartite synapses using super-resolution microscopy”.
Project 15: “Nanoscale organization and dynamics of synapsin condensates”

For more information on projects and techniques which will be taught at the course, download the projects list.

Bordeaux School of Neuroscience, France

Registration

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

Application call closed on 5 July 2021

Course sponsors

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

Weizmann Institute of Science

Israel

Stanford University

USA

Center for Molecular Neurobiology Hamburg (ZMNH)

Germany

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

Registration

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

Application closed on 7 December 2020

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

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

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.

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

Open Ephys Production Site, PT

MIT and Open Ephys, USA

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.

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.

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

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

Registration

Course overview

Course sponsors

What will you learn?

Faculty

Alex Leighton

Jakob Voigts

Filipe Carvalho

Instructors

Programme

Day 1 – Introduction

Day 2 – Impedance

Day 3 – Data Acquisition

Day 4 – Synchronizing Datastreams

Day 5 – Project and Open-Source Neuroscience

Registration

Course overview

Course directors

Luísa V. Lopes

Cheryl L. Grady

Nora Abrous

Keynote Speakers

Instructors

Course content

Projects

Bordeaux School of Neuroscience, France

Registration

Course overview

Course Partners

What will you learn?

Course directors

Programme

Day 1 – Sensors and Motors

Day 2: Microcontrollers and Programming

Day 3: Computers and Programming

Day 4: (Machine) Vision

Day 5: (Machine) Learning

Registration

Course overview

Course partner

Dimitri Rusakov

Tatiana Korotkova

Grégory Giannone

Course content

Topics & Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course sponsors

Course overview

Course partner

Course directors

Keynote speakers

Instructors

Course content

Topics & Techniques

Projects

Bordeaux School of Neuroscience, France

Registration

Course sponsors

Course overview

Course sponsors

What will you learn?

Faculty

Alex Leighton

Jakob Voigts

Filipe Carvalho