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Module 5: Calcium Imaging

Mike X. Cohen

In this course, you will learn about working with calcium-imaging data, including image processing to remove background "blur", identifying cells based on threshold spatial contiguity, time-series filtering, and principal component analysis (PCA). The MATLAB code shows data animations, capabilities of the image processing toolbox, and PCA.

 
INCF TrainingSpace

Computational Neuroscience: The Basics

INCF

This course consists of a series of lessons which aim to introduce the basic conceptual and experimental approaches in computational neuroscience. 

 

Research, Ethics, and Societal Impact

HBP Education Programme

This course explores ethical and social issues that have arisen, and continue to arise, from the rapid research development in neuroscience, medicine, and ICT. Lectures focus on key ethical issues contained in the HBP – such as the ethics of robotics, dual use, ICT ethical issues, big data and individual privacy, and the use of animals in research.

 

Data Science and Reproducibility

Michel Dumontier

This brief course consists of slides on data science and reproducibility issues from lectures given at Maastricht University. 

 
INCF TrainingSpace

Basic Mathematics for Computational Neuroscience

Alex Williams

A series of short explanations of the basic equations underlying computational neuroscience.

 
INCF TrainingSpace

Deep Learning: Parameters Sharing

NYU Center for Data Science

This course covers the concepts of recurrent and convolutional nets (theory and practice), natural signals properties and the convolution, and recurrent neural networks (vanilla and gated, LSTM).

 

TVB Made Easy

The Virtual Brain

In this short series of lectures, participants will take a look at articles using TVB in a clinical context. Specifically, participants will see how TVB can help to predict recovery after stroke and how individual epileptic seizures are simulated. The course lecturers will briefly describe the methods used and results achieved in the articles.

 

Cognitive Science and Psychology: Mind, Brain, and Behavior

NeurotechEU

This lecture series is presented by NeuroTechEU, an alliance between eight European universities with the goal to build a trans-European network of excellence in brain research and technologies. By following along with this series, participants will learn about the history of cognitive science and the development of the field in a sociocultural context, as well as its trajectory into the future with the advent of artificial intelligence and neural network development.

 

Fundamental Methods for Single-Cell Transcriptome Analysis

Krembil Centre for Neuroinformatics

This course, consisting of one lecture and two workshops, is presented by the Computational Genomics Lab at the Centre for Addiction and Mental Health and University of Toronto. The lecture deals with single-cell and bulk level transciptomics, while the two hands-on workshops introduce users to transcriptomic data types (e.g., RNAseq) and how to perform analyses in specific use cases (e.g., cellular changes in major depression). 

 

Fundamental Methods for Genomic Analysis

Krembil Centre for Neuroinformatics

This course includes both lectures and tutorials around the management and analysis of genomic data in clinical research and care. Participants are led through the basics of genome-wide association studies (GWAS), genotypes, and polygenic risk scores, as well as novel concepts and tools for more sophisticated consideration of population stratification in GWAS.

 

The International Brain Initiative (IBI)

INCF

The International Brain Initiative (IBI) is a consortium of the world’s major large-scale brain initiatives and other organizations with a vested interest in catalyzing and advancing neuroscience research through international collaboration and knowledge sharing. This session will introduce the IBI and the current efforts of the Data Standards and Sharing Working Group with a view to gain input from a wider neuroscience and neuroinformatics community. 

 

FAIR Approaches for Computational Neuroscience

INCF

As models in neuroscience have become increasingly complex, it has become more difficult to share all aspects of models and model analysis, hindering model accessibility and reproducibility. In this session, we will discuss existing resources for promoting FAIR data and models in computational neuroscience, their impact on the field, and remaining barriers.

 

Simulating Brain Microcircuit Activity and Signals in Mental Health

Krembil Centre for Neuroinformatics

This course offers lectures on the origin and functional significance of certain electrophysiological signals in the brain, as well as a hands-on tutorial on how to simulate, statistically evaluate, and visualize such signals. Participants will learn the simulation of signals at different spatial scales, including single-cell (neuronal spiking) and global (EEG), and how these may serve as biomarkers in the evaluation of mental health data.

 
INCF TrainingSpace

Deep Learning: Graphs

NYU Center for Data Science

This module provides an introduction to the problem of speech recognition using neural models, emphasizing the CTC loss for training and inference when input and output sequences are of different lengths. It also covers beam search for use during inference, and how that procedure may be modeled at training time using a Graph Transformer Network.

 

Digital Health for Mental Health

Krembil Centre for Neuroinformatics

As technological improvements continue to facilitate innovations in the mental health space, researchers and clinicians are faced with novel opportunities and challenges regarding study design, diagnoses, treatments, and follow-up care. This course includes a lecture outlining these new developments, as well as a workshop which introduces users to Synapse, an open-source platform for collaborative data analysis. 

 
INCF TrainingSpace

Deep Learning: Associative Memories

NYU Center for Data Science

This module covers the concept of associative memories in deep learning. It is a part of the Deep Learning Course at NYU's Center for Data Science. Prerequisites for this module include: Introduction to Deep Learning (module 1 of the course), Parameter Sharing (module 2 of the course), 

 

Using brainlife.io

brainlife.io

This course provides several visual walkthroughs documenting how to execute various processes in brainlife.io, an open-source, free and secure reproducible neuroscience analysis platform. The platform allows to analyze Magnetic Resonance Imaging (MRI), electroencephalography (EEG) and magnetoencephalography (MEG) data. Data can either be uploaded from local computers or imported from public archives such as OpenNeuro.org.

 

The Virtual Brain: Bernstein Center Lectures 2019

The Virtual Brain

This course provides a general overview about brain simulation, including its fundamentals as well as clinical applications in populations with stroke, neurodegeneration, epilepsy, and brain tumors. This course also introduces the mathematical framework of multi-scale brain modeling and its analysis.

 

INCF Short Course: Introduction to Neuroinformatics

INCF

The emergence of data-intensive science creates a demand for neuroscience educators worldwide to deliver better neuroinformatics education and training in order to raise a generation of modern neuroscientists with FAIR capabilities, awareness of the value of standards and best practices, knowledge in dealing with big datasets, and the ability to integrate knowledge over multiple scales and methods.

 

FAIR Approaches for Neuroimaging Research

INCF

Over the last three decades, neuroimaging research has seen large strides in the scale, diversity, and complexity of studies, the open availability of data and methodological resources, the quality of instrumentation and multimodal studies, and the number of researchers and consortia. The awareness of rigor and reproducibility has increased with the advent of funding mandates, and with the work done by national and international brain initiatives.