The Multi-scale brain

The Multi-scale brain

28 h
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  • 7 Sequences
  • Advanced Level

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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


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


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
Staff Scientist
École polytechnique fédérale de Lausanne


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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