The Multi-scale brain
list 7 sequences
assignment Level : Advanced
chat_bubble_outline Language : English
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timer 28 hours in total

About the content

Understanding the brain requires an integrated understanding of different scales of organisation of the brain. This means studying the role that genes, channels, cells, microcircuits, and even whole brain regions have in different types of behaviour: From perception to action, while asleep or when being awake.

This course will take the you through the latest data, models and techniques for investigating the different levels of the brain. We will show how we can put the pieces together and attain new insights and derive new theories. With contributions from more than 10 international neuroscientists from six different research institutions, the MOOC gives a broad overview of the latest tools and techniques for neuroinformatics, analysis, modelling and simulation.
At the same time, several different tutorials on available data and data tools, such as those from the Allen Institute for Brain Science, provide you with in-depth knowledge on brain atlases, gene expression data and modeling neurons. These tutorials will be followed by exercises that give you the opportunity to acquire the necessary skills to use the tools and data for your own research.

  • How to explain and contrast different techniques for visualization, mapping, and modeling of single cells, synaptic fields, larger circuits of neurons, and long-range interactions between cortical areas
  • Ways to classify neurons and relate cell morphology to function
  • How to use brain atlases and modeling tools

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Knowledge of ordinary differential equations, and their numerical solution.
Knowledge of programming in one of the following: Python (preferred), C/C++, Java, MATLAB, R.



1.     Introduction

1.1.   Introduction to the course, Sean Hill
1.2.   Introduction to the Allen Institute for Brain Science data and tools, Terri Gilbert
1.3.   Human Brain Atlasing, Danilo Bzdok
1.4.   Graded quiz 1

2.    Genetic Mapping of the mouse brain

2.1.   Using whole-brain and single-cell gene expression to identify and characterize cell types, Vilas Menon
2.2.   Genetic dissection of neural circuits, Trygve Bakken

3.     Navigating gene expression data.

3.1.   Accessing mouse gene expression data, Terri Gilbert
3.2.   Navigating the human gene expression data, Terri Gilbert 
3.3.   Peer-graded assignment gene expression data

4.     Multi-scale connectivity

4.1.   Synaptic Mapping with Array Tomography, Forrest Collman
4.2.   Mesoscale mapping, Jack Waters
4.3.   The connectivity atlas, Terri Gilbert
4.4.   Graded assignment mouse connectivity

5.     Multi-scale modeling

5.1.   Blue Brain, Sean Hill
5.2.   Cell types and modeling, Werner von Geit & Elisabetta Iavarone
5.3.   Graded assignment modeling
5.4.   Building bio-physiologically constrained models of large-scale phenomena in the brain, Alain Destexhe
5.5.   Graded quiz 2

6.     Reconstructing micro-circuitry

6.1.   Computational properties of human cortical microcircuits Huib Mansvelder
6.2.   Modelling microcircuits, Michael Reimann
6.3.   Graded quiz 3

7.     Structure and function of the whole brain

7.1.  Whole brain morpho-functional imaging: connecting a single neuron to whole brain, Francesco Pavone
7.2.   Functional physiology of the mouse virtual cortex, Saskia de Vries
7.3.   Brain observatory data sets, Terri Gilbert
7.4.   Peer-graded homework
7.5.   Graded quiz 4

8. Final exam


Sean Hill
École polytechnique fédérale de Lausanne

Terri Gilbert
Gilhou Scientific Communications

Forrest Collman
Allen Institute for Brain Science

Trygve Bakken
Allen Institute for Brain Science

Saskia de Vries
Allen Institute for Brain Science

Jack Waters
Allen Institute for Brain Science

Huib Mansvelder
Center for Neurogenomics and Cognitive Research

Vilas Menon
Janelia research campus

Alain Destexhe
Le Centre national de la recherche scientifique

Francesco Pavone
École polytechnique fédérale de Lausanne

Danilo Bzdok
RWTH Aachen University

Michael Reimann
École polytechnique fédérale de Lausanne


Content designer

The École polytechnique fédérale de Lausanne (EPFL, English: Swiss Federal Institute of Technology in Lausanne) is a research university in Lausanne, Switzerland, that specialises in physical sciences and engineering.

One of the two Swiss Federal Institutes of Technology, the school was founded by the Swiss Federal Government with the stated mission to:

Educate engineers and scientists to the highest international standing
Be a national center of excellence in science and technology
Provide a hub for interaction between the scientific community and the industry
EPFL is considered one of the most prestigious universities in the world for engineering and sciences, ranking 17th overall and 10th in engineering in the 2015 QS World University Rankings; 34th overall and 12th in engineering in the 2015 Times Higher Education World University Rankings.



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