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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
neurons green blue

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)

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

man benjamin

Benjamin de Bivort

Course Director

Harvard University, USA

woman ann

Ann Kennedy

Course Director

Northwestern University, USA

man giorgio

Giorgio Gilestro

Course Director

Imperial College London, UK

Daniel McNamee

Course Director

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)
Iain Couzin (Max Planck Institute, Konstanz, Germany)
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)
Hugo Spiers (UCL, UK)
Nachum Ulanovsky (Weizmann Institute, Israel)

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

QAB 2

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.

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.

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

Man alfonso

Alfonso Renart

Course Director

Champalimaud Research, Portugal

Geffen

Maria Geffen

Course Director

University of Pennsylvania, USA

Brent Doiron

Course Director

University of Chicago, USA

Gjorgjieva

Julijana Gjorgjieva

Course Director

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

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

Applications now open.

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

Advanced Imaging Techniques for Neuroscience

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.

Valentin Nägerl

Course Director

University of Bordeaux, France

University of Göttingen, Germany

Jan Huisken

Co-Director

University of Göttingen, Germany

Keynote speakers

Will be announced soon.

Instructors

Will be announced soon.

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:

  1. Teach students the theoretical foundation of advanced imaging techniques for molecular, cellular and systems neuroscience research.

  2. 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.

  3. 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

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

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

Registration

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

Applications will open soon.

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.

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. We will provide 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. Thus, this course will combine theoretical and methodological courses by keynote speakers and instructors, respectively, with hands-on projects conducted in the Bordeaux School of Neuroscience.

Course directors

University of Copenhagen, Denmark

Paris Brain Institute, France

University of Bordeaux, France

Seminal Lecture

Dr. Réjean Dubuc – Université de Montréal, Canada

Honorary lectures from Brain Prize Winners

Dr. Sylvia Arber – Basel University, Switzerland
Dr. Ole Kiehn – University of Copenhagen, Denmark

Keynote Speakers

Dr. David McLean – Northwestern University, USA
Dr. Claire Wyart – Sorbonne Université, France
Dr. Lora Sweeney – Institute of Science and Technology A., Austria
Dr. Janathan Whitlock – KISN, Norway
Dr. Camille Jeunet – CNRS, Université of Bordeaux, France
Dr. Marie-Laure Welter – Université Pierre et Marie Curie, France
Dr. Joaquim Alves da Silva – Champalimaud CU, Portugal
Dr. Gilad Silberberg – Karolinska Institutet, Sweden
Dr. Claire Meehan – University of Copenhagen, Denmark
Dr. Ian Duguid – University of Edinburgh, UK
Dr. Rune Berg – University of Copenhagen, Denmark

Instructors

Will be announced soon.

Course content

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.

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications will open soon.

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.

Neuro-vascular function in health and disease

Course overview

The neurovascular unit, composed of vascular cells, glial cells, and neurons is fundamental for the proper function of the brain. The NVU regulates supply of the cerebral blood flow (CBF) and maintains integrity of the blood-brain barrier (BBB).

Dysfunction of the neurovascular unit may result in devastating conditions such as dementia, cerebral ischemia, or brain oedema formation. This advanced experimental course will allow students to gain basic knowledge and hands-on experience on the most important techniques used to study the neurovascular unit, such as in vivo/in vitro high-resolution imaging, magnetic resonance imaging, and rodent models of cerebrovascular disease. The course will also focus on data reproducibility and open science.

Course partner

Course directors

Nikolaus Plesnila

Course Director

Ludwig Maximilian University, Germany

Jérôme Badaut

Course Director

Bordeaux University, France

Catherine Hall

Course Director

Sussex University, UK

Keynote Speakers

David Attwell – University College London, UK
Felipe Barros – Centro de Estudios Científicos, Chile
Serge Charpak – University of Paris, France
Turgay Dalkara – Hateceppe University, Turkey
Ali Ertürk – University of Munich, Germany
Jean Francois Ghersi-Egea – Lyon Neuroscience Research Centre, France
Anne Joutel – University of Paris, France
Martin Lauritzen – University of Copenhagen, Denmark
Malcolm MacLeod – University of Edinburgh, UK
Pierre Magistretti – University of Lausanne, Switzerland
Maiken Nedergaard – University of Copenhagen, Denmark
Mark Nelson – University of Burlington, USA
Andy Obenhaus – USI, USA
Andy Shih – Seattle Children’s Research Institute, USA
Robert Thorne – Denali Therapeutics / University of Wisconsin-Madison, USA
Susanne Van Veluw – Harvard Medical School, USA

Instructors

Silvia Anderle – University of Sheffield
Orla Bonnar – University of Sheffield
Gian-Marco Calandra – Massachusetts General Hospital
Audrey Chagnot – University of Sussex
Yulia Dembitskaia – University of Edinburgh
Maximillian Dorok – Johns Hopkins
Christophe Dubois – université de Bordeaux
Beth Eyre – University of Munich
Severin Filser – University of Munich
Jordan Girard – Université de Bordeaux
Clare Howarth – University of Munich
Malika Ihle – University of Munich
Igor Khalin – University of Munich
Tom Langdon – University of Munich
Guillaume Le Bourdelles – Inscopix
Axel Montagne – Université de Bordeaux
Burcu Seker – Université de Bordeaux
Josh Shrouder – University of Munich
Rebecca Sienel – University of Edinburgh
Jonathan Zapata – Johns Hopkins

Course content

This 3-week long course is a practical “hands-on” introduction to advanced methods for the investigation of the neuro-vascular unit in health and disease. The course will be structured in a theoretical and a practical part.

In the theoretical part world leading scientists in the neurovascular unit (NVU) research will give overview lectures about the function of the NVU and present techniques how to study the NVU in a reproducible manner. Such overview presentations will be paralleled by workshops. In the practical part of the course students will learn surgical techniques necessary to perform animal models of disease and to prepare cranial windows required for the study of cerebral vessels, will be trained to image cerebral vessel function in vitro and in vivo, and will learn how to analyse and display the acquired data.

Techniques

The following techniques will be taught at the course:

  • Chronic cranial window surgery

  • Habituation to the rig for awake imaging

  • Experimental design and presentation of stimuli

  • 2 photon imaging of neurovascular coupling (neuronal activity, blood vessel dilations)

  • 2 photon imaging of vascular function (vasomotion, calcium signals in vessels)

  • Wide field imaging and recording of neurovascular function and metabolism (2D OIS, laser speckle, haemoglobin spectrometry, laser doppler flowmetry – equipment to be loaned by Moor Instruments)

  • Data processing and analysis

Projects

The following projects will be taught at the course:

  • Two-photon microscopy imaging of blood vessels and neuronal activity in vivo

  • Brain imaging in freely moving mice using mini-scopes

  • Two-photon microscopy imaging of stroke

  • Widefield imaging of neurovascular relationships

  • Open Science

  • Correlative light-electron microscopy (CLEM)

  • Vascular signalling in pressurized brain slices

  • BBB permeability in mice and humans by MRI

  • SUSHI – evaluating the brain’s extracellular space by STED microscopy

  • Histological techniques for the analysis of cerebral vessels

  • Brain clearing for the analysis of cerebral vessels

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications closed on 14 November 2022

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

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

Course sponsors

Interacting with neural circuits

Course overview

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

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

Course directors

Michael Hausser

Course Director
UK

Susana Lima

Course Director
Portugal

Tiago Branco

Course Director
UK

Executive director

Pedro Garcia da Silva

Course Executive Director
Portugal

Keynote Speakers

Instructors

Stan Heinze – Lund University, Sweden
Chris Xu
Cornell University, USA
Michael Orger – Champalimaud Foundation, Portugal
Constanze Lenschow
– Magdeburg University, Germany
Ana João Rodrigues
– ICVS, Minho University, Portugal
Bob Datta
– Harvard University, USA
Marta Moita
– Champalimaud Foundation, Portugal
Botond Roska – Institute of Molecular and Clinical Ophthalmology Basel, Switzerland
Tobias Rose – University of Bonn Medical Center, Germany
Darcy Peterka
– Columbia University, USA
Vanessa Ruta –
Rockefeller University, USA
Eugenia ChiappeChampalimaud Foundation, Portugal
Isaac Bianco
University College of London, UK
Christine Constantinople
– New York University, USA
Nicolò Accanto
– Institut de la Vision, France
Carsen Stringer
– HHMI Janelia, USA
Greg Jefferis
– MRC Laboratory of Molecular Biology, UK
Nick Steinmetz
– University of Washington, USA
Michael Brecht
– Bernstein Center for Computational Neuroscience, Germany

Course content

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

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

Champalimaud Centre for the Unknown, Portugal

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

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

Registration

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

Applications closed on 31 January 2023

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

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

Sponsors

Supported by a gift from the Simons Foundation

Glial cells in health and diseases

Course overview

For over a century, the main focus of neuroscience research has been on neurons. It is however, becoming ever more clear that brain functions such as conceptual reasoning, memory, and processing speed depend on glial cells (microglia, astrocytes and oligodendrocytes).

The lack of understanding of the role of glia in normal brain development, function and disease is mainly due to lack of tools and methods to accurately study these cells. In recent years, neuroscience has seen a methodological revolution. The function of glia cells in neuronal circuit development, and neurodegenerative disease has become evident. The study of glial biology and the understanding on how glial cells impact on circuit function are key to understanding how the brain works and what goes wrong in brain disease. Advanced training of a new generation of neuroscientists with strong focus on glial function is crucial to make these studies a success in the coming decades.

Course directors

Cambridge University, UK

Cagla Eroglu

Course Director

Duke University, US

Staci Bilbo

Course Director

Duke University, US

Bordeaux Neurocampus, FR

Keynote Speakers

Amit Agarwal – Heidelberg University, Germany
Paola Arlotta – Harvard University, US
David Belin – University of Cambridge, UK
Bart J. L. Eggen – University Medical Center Groningen, The Netherlands
Sonia Garel – Institut de Biologie de l’Ecole Normale Superieure (IBENS), Paris, France
Soyon Hong – UCL, London, UK
Maarten Kole – Utrecht University, The Netherlands
Kelly Monk – The Vollum Institute, OHSU, US
Stéphane Oliet – Neurocentre Magendie, France
Thomas Papouin – Washington University School of Medicine in St. Louis, US
Nathalie Rouach – College de France, France
David Rowitch – University of Cambridge, UK
Mikael Simons – Technical University Munich, Germany

Instructors

Amit Agarwal – Heidelberg University, Germany
Liam BarryCarroll – IMN, Bordeaux Neurocampus, France
Arne Battefeld – IMN, Bordeaux Neurocampus, France
Felipe Bodaleo – Heidelberg University, Germany
Sarah Bou Sader Nehme – IMN, Bordeaux Neurocampus, France
Sara Carracedo Vicente – IMN, Bordeaux Neurocampus, France
Omar De Faria – Stem Cell Institute, University of Cambridge, UK
Mohit Dubey – Netherlands Institute for Neuroscience, The Netherlands
Jiaxing Li – Oregon Health & Science University, US
Charlotte Madore-Delpech – INRAE, University of Bordeaux, France
Giampaolo Milior – College de France, France
Wiebke Möbius – Max Planck Institute for Multidisciplinary Sciences, Germany
Torben Ruhwedel – Max Planck Institute for Multidisciplinary Sciences, Germany
Kristina Sakers Hays – Duke University Medical Center, US
Caroline Smith – Boston College, US
Francesco Ulloa Severino – Duke University, US

Course content

This is a theoretical and practical training course on glial cells and their communication with neuronal circuits. It will provide an overview of the current concepts and knowledge of glial cell biology in central and peripheral nervous system development in several species, including zebrafish, mice, and humans, and their link to diseases.

It will combine lectures and hands-on projects on glial development including methods in cellular neuroscience (e.g. live and fixed tissue imaging), genetic modifications, -omics (e.g., scRNA seq, proteomics and bioinformatics), electrophysiology, optogenetic and chemogenetic manipulation of glial cells and methods to study behaviour.

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.

Sponsors

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.

Machine learning for neuroscience

Course overview

Neuroscience has played an important role in the history of Artificial intelligence and Machine learning. Artificial neural networks are inspired by neuronal physiology and are today the core of Deep Learning. This common history continues today. Machine Learning methods are developed into tools that allow for a higher quality of data processing in the study of animal behavior and brain activity. Machine Learning is also used to model the brain as it can solve similar problems to what brains solve and the basic units of processing may be comparable.

The course gives a hands-on introduction to Artificial Intelligence and Machine Learning and how it can be used for data acquisition, analysis and modeling brain activity and behavior. Experts in the field will teach the basics of Machine Learning and how to apply it to Neuroscience and will also discuss the limits of the field, and what are the boundaries of application and how Neuroscience and Psychology could inform new systems.

Course directors

Gonzalo de Polavieja

Course Director

Champalimaud Foundation, PT

Kristin Branson

Course Director

HHMI Janelia, USA

Il Memming Park

Course Director

Champalimaud Foundation, PT

Keynote Speakers

Ann Kennedy – Northwestern University, US
N. Alex Cayco Gajic – École Normale Supérieure, France
Ben Cowley – Cold Spring Harbor, US
Kim Stachenfeld – DeepMind, UK
Jennifer Sun Caltech, US
Josue Nassar – Stony Brook University, US
Laura Driscoll – Stanford University, US
Maneesh Sahani Gatsby Computational Neuroscience Unit, UK
Nakul Verma – Columbia University, US
Patrick Mineault – xcorr, Canada
Rui Ponte Costa – University of Oxford, UK
Sara Solla – Northwestern University, US
Surya Ganguli Stanford University, US

Instructors

Course content

Programme

During the first two weeks, there will be lectures in the morning, and evening tutorials will consist of analytical and computational application of the concepts learned in the morning. The third week consists of lectures in the mornings and projects in the evening.

First week

The first week will consist of a mini-course in Machine Learning, especially those techniques used in Neuroscience. This will include supervised and unsupervised learning, learning for time series and Reinforcement Learning, as well as a day dedicated to practical aspects in the use of Machine Learning Techniques.

Day 1: History of AI and the relationship between Machine Learning and Neuroscience
Day 2: Supervised Learning
Day 3: Unsupervised Learning
Day 4: Practical consideration of the use of Machine Learning
Day 5: Learning for Time Series
Day 6: Reinforcement Learning

Second Week

The second week discusses how Machine Learning techniques are applied in Neuroscience. This will include the Machine Learning tools used to extract information from datasets of animal behavior and brain activity, Machine Learning models from brain activity and behavior, models using spiking neural networks and which are the limits ofML techniques.

Day 7: ML tools in animal behavior
Day 8: ML tools in brain activity
Day 9: Models derived from the brain and behavior
Day 10: ML-based models of the brain & discrepancies
Day 11: Theory-based modeling, and its connection to ML
Day 12: Bio-inspired ML/spiking networks

Third week

The third week has lectures on more advanced topics and evenings on projects.

Students will design projects applying machine learning (ML) methods to neural recording and animal behavior data sets. Neural recording data sets provided will be from a variety of techniques, including electrophysiology, calcium imaging, and fMRI. Behavior data sets provided will be from video. Students may focus on developing new ML algorithms for improving automated tracking, segmentation, categorization, or representation learning. Alternatively, they may focus on applying these ML methods to large data sets to discover new biological insights. A third option is to explore ML-based computational models of neural activity or behavior. Through these projects, students will gain hands-on experience using modern ML approaches, coding in PyTorch, and gain a deeper understanding of the power and potential failures of ML.

Datasets

Behavioral Datasets

  • Fish Fish in groups, raw and tracked
  • Some rodents and ants, raw and tracked
  • Flies data from Maabe and other datasets.

Neural Datasets (spike trains)

  • Neural Latent Benchmark ones
  • Neuromatch ones (e.g. Steinmetz)
  • Brain machine interface related datasets
  • IBL datasets

Other Neural Datasets ( LFP, fMRI, etc)

Computational models (not datasets but used as input for further analysis or modeling)

  • RNNs trained on tasks
  • Models trained on fish in collectives

Techniques

  • Deep learning tools for analyzing complex behavior data

  • Neural manifolds

  • Modeling neural computation with recurrent neural networks

  • State space modeling of neural time series

  • Probabilistic modeling of neural data and behavior

  • Deep learning models of brain activity and behavior

  • Spiking neural networks

  • Best practices for high quality neuroscience research using machine learning

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 : €2.950,00 (includes tuition fee, accommodation and meals)

Applications closed on 23rd January 2023

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

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

Sponsors

Connectomics from micro- to meso- and macro-scales

Course overview

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

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

Course directors

Gregory Jefferis

Course Director

MRC LMB and University of Cambridge, UK

Jinny Kim

Course Director

Korea Institute of Science and Technology, Korea

Nicolas Renier

Course Director

Paris Brain Institute, France

Allen Institute of Brain Science, US

Keynote Speakers

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

Instructors / Teaching Assistants

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

Course content

Light Microscopy and functional, molecular methods:

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

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

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

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

Electron microscopy synaptic connectomics:

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

Techniques

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

Projects

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

Bordeaux School of Neuroscience, France

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

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

Registration

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

Applications closed 17 April 2023

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

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