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The Multi-scale brain

5,603 people completed this program


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 coursewill 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


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

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The Multi-scale brain
7 weeks
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