The Multi-scale brain from edX

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.

What's inside

Learning objectives

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

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

Syllabus

1. Introduction

2. Genetic Mapping of the mouse brain

3. Navigating gene expression data.

4. Multi-scale connectivity

5. Multi-scale modeling

6. Reconstructing micro-circuitry

7. Structure and function of the whole brain

8. Final exam

1.1. Introduction to the course, Sean Hill1.2. Introduction to the Allen Institute for Brain Science data and tools, Terri Gilbert1.3. Human Brain Atlasing, Danilo Bzdok1.4. Graded quiz 1

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

3.1. Accessing mouse gene expression data, Terri Gilbert3.2. Navigating the human gene expression data, Terri Gilbert3.3. Peer-graded assignment gene expression data

4.1. Synaptic Mapping with Array Tomography, Forrest Collman4.2. Mesoscale mapping, Jack Waters4.3. The connectivity atlas, Terri Gilbert4.4. Graded assignment mouse connectivity

5.1. Blue Brain, Sean Hill5.2. Cell types and modeling, Werner von Geit & Elisabetta Iavarone5.3. Graded assignment modeling5.4. Building bio-physiologically constrained models of large-scale phenomena in the brain, Alain Destexhe5.5. Graded quiz 2

6.1. Computational properties of human cortical microcircuits Huib Mansvelder6.2. Modelling microcircuits, Michael Reimann6.3. Graded quiz 3

7.1. Whole brain morpho-functional imaging: connecting a single neuron to whole brain, Francesco Pavone7.2. Functional physiology of the mouse virtual cortex, Saskia de Vries7.3. Brain observatory data sets, Terri Gilbert7.4. Peer-graded homework7.5. Graded quiz 4

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Explores practical applications and career paths in neuroscience

Taught by Sean Hill and Terri Gilbert, both renowned experts in neuroinformatics and neuroscience

Examines brain function across multiple scales, from genetic to behavioral

Develops skills in data analysis, visualization, and modeling of brain data

Involves contributions from over ten international neuroscientists

Provides hands-on experience with neural data and tools through tutorials and exercises

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in The Multi-scale brain with these activities:

Read 'Principles of Neural Science'

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Strengthen your understanding of the fundamental principles of neuroscience by reading a comprehensive textbook.

View Principles of Neural Science, Fifth Edition... on Amazon

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Read specific chapters or sections relevant to the course topics.
Summarize key concepts and make notes.
Discuss the book's content with peers or the instructor.

Review of Cell Biology and Neuroscience

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Review the basics of cell biology and neuroscience to strengthen your foundation for understanding the brain.

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Revisit textbooks and notes from previous courses in cell biology and neuroscience.
Attend online lectures or workshops on cell biology and neuroscience.
Complete practice problems or quizzes to test your understanding.

Using the Allen Institute Atlases and Tools

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Become familiar with the Allen Institute for Brain Science's extensive data resources and learn how to use their tools effectively.

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Explore the Allen Institute website and familiarize yourself with their data offerings.
Follow guided tutorials on navigating the atlases and using specific tools.
Practice using the tools to explore gene expression data, connectivity data, and brain regions.
Attend webinars or workshops hosted by the Allen Institute.

Four other activities

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Practice Identifying and Classifying Neurons

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Develop your ability to identify and classify neurons based on their structure and function.

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Examine images of different neuron types and identify their key features.
Complete online quizzes or interactive exercises on neuron classification.
Practice applying classification criteria to real-world examples.
Attend a workshop or lab session focused on neuron identification.

Discuss Applications of Brain Mapping Techniques

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Engage with peers to explore the practical applications of brain mapping techniques in various fields.

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Form study groups or join online forums.
Discuss different brain mapping techniques and their advantages, limitations, and applications.
Share research findings and case studies related to brain mapping.
Guest: Invite a researcher or expert in brain mapping to share their insights.

Build a Model of a Neural Circuit

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Apply your knowledge of neural circuits and modeling to create a functional model that simulates a specific brain function.

Browse courses on Neural Circuits

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Choose a specific neural circuit or brain function to model.
Select appropriate software or tools for building the model.
Design and implement the model, including defining parameters and simulating behavior.
Validate the model by comparing its output to experimental data or known behaviors.
Present your model and findings to peers or instructors for feedback.

Attend a Workshop on Computational Neuroscience

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Deepen your understanding of computational approaches to studying the brain by attending a specialized workshop.

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Research and identify relevant workshops.
Register and attend the workshop.
Engage actively in discussions and hands-on activities.
Apply the knowledge gained to your own research or projects.

Career center

Learners who complete The Multi-scale brain will develop knowledge and skills that may be useful to these careers:

Computational Neuroscientist

Computational Neuroscientists use computer models to study the brain. This course will help future Computational Neuroscientists to build a foundation in neuroscience and to understand how to work with brain data. Computational Neuroscientists who are well-versed in brain data will be more likely to succeed in developing new models of the brain and in using these models to understand the brain and to treat brain disorders.

See salaries and explore the career path for Computational Neuroscientist

Neurosurgeon

Neurosurgeons operate on the brain and nervous system. This course will help future Neurosurgeons to build a foundation in neuroscience and to understand how to work with brain data. Neurosurgeons who are well-versed in brain data will be more likely to succeed in diagnosing and treating neurological disorders.

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Neurologist

Neurologists diagnose and treat disorders of the nervous system, including the brain. This course will help future Neurologists to build a foundation in neuroscience and to understand how to work with brain data. Neurologists who are well-versed in brain data will be more likely to succeed in diagnosing and treating neurological disorders.

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Cognitive Scientist

Cognitive Scientists study the mind and how it works. This course will help future Cognitive Scientists to build a foundation in neuroscience and to understand how to work with brain data. Cognitive Scientists who are well-versed in brain data will be more likely to succeed in understanding the mind and how it works.

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Neuroengineer

Neuroengineers design and develop devices that interact with the nervous system. This course will help future Neuroengineers to build a foundation in neuroscience and to understand how to work with brain data. Neuroengineers who are well-versed in brain data will be more likely to succeed in designing and developing new devices that can help us to understand the brain and to treat brain disorders.

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Bioinformatician

Bioinformaticians use computer science to analyze biological data. This course will help future Bioinformaticians to build a foundation in neuroscience and to understand how to work with brain data. Bioinformaticians who are well-versed in brain data will be more likely to succeed in developing new methods for analyzing brain data and in using this data to understand the brain and to treat brain disorders.

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Psychiatrist

Psychiatrists diagnose and treat mental disorders. This course will help future Psychiatrists to build a foundation in neuroscience and to understand how to work with brain data. Psychiatrists who are well-versed in brain data will be more likely to succeed in diagnosing and treating mental disorders.

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Neuroethicist

Neuroethicists study the ethical implications of neuroscience research and applications. This course will help future Neuroethicists to build a foundation in neuroscience and to understand how to work with brain data. Neuroethicists who are well-versed in brain data will be more likely to succeed in understanding the ethical implications of neuroscience research and applications.

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Computer Scientist

Computer Scientists design and develop computer systems and applications. This course will help future Computer Scientists to build a foundation in neuroscience and to understand how to work with brain data. Computer Scientists who are well-versed in brain data will be more likely to succeed in designing and developing computer systems and applications that can help us to understand the brain and to treat brain disorders.

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Research Scientist

Research Scientists conduct scientific research to advance knowledge in a particular field. This course will help future Research Scientists to build a foundation in neuroscience and to understand how to work with brain data. Research Scientists who are well-versed in brain data will be more likely to succeed in academia, industry, and government.

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Healthcare Consultant

Healthcare Consultants help healthcare organizations improve their performance. This course will help future Healthcare Consultants to build a foundation in neuroscience and to understand how to work with brain data. Healthcare Consultants who are well-versed in brain data will be more likely to succeed in helping healthcare organizations to improve their performance in the areas of neuroscience and brain health.

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Science Writer

Science Writers communicate scientific information to the public. This course will help future Science Writers to build a foundation in neuroscience and to understand how to work with brain data. Science Writers who are well-versed in brain data will be more likely to succeed in communicating scientific information about the brain to the public.

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Data Analyst

Data Analysts help businesses analyze and understand their data to make informed decisions. This course will help future Data Analysts to build a foundation in data science and to understand how to work with brain data. Data Analysts who are well-versed in brain data will be more likely to succeed in the healthcare, education, government, and other industries that rely heavily on this data.

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Neuromarketer

Neuromarketers use neuroscience to understand consumer behavior. This course will help future Neuromarketers to build a foundation in neuroscience and to understand how to work with brain data. Neuromarketers who are well-versed in brain data will be more likely to succeed in understanding consumer behavior and in developing marketing campaigns that are more effective.

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Data Scientist

Data Science is the field of interpreting raw data to find patterns and gain insights. Data Scientists do this by using automated methods, such as machine learning. Understanding how to use brain data for AI is a key part of Data Science today. This course allows the Data Scientist to understand how brain data is structured, which techniques can be applied to it, and how to interpret the output of these techniques. It does this by providing data from the Allen Institute for Brain Science, and then by presenting use cases and tools for interpreting this data.

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