HIBALL Winter School 2021

Day 1 - 01. Opening Address

Katrin Amunts, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany opening the first HIBALL Winter School on BigBrain data and tools, Feb 3, 2021

Day 1 - 02. BigBrain anatomy for beginners

Nicola Palomero-Gallagher, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

The goal of this course is to familiarize scientists with no, or only very little, knowledge about brain anatomy with major brain structures and their functions.

Day 1 - 03. Joint infrastructure for BigBrain

Petur Helgi Einarsson, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Germany, and School of Engineering and Natural Sciences of the University of Iceland

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 04. Short introduction to DataLad and Jülich activities

Morris Riedel, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Germany, and School of Engineering and Natural Sciences of the University of Iceland

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 05. Hands-on: BigBrain data processing with CBRAIN and DataLad

Tristan Glatard, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 06. Hands-on: Processing BigBrain datasets with Boutiques

Valérie Hayot-Sasson, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 07. Hands-on: Contributing datasets to archives using DataLad

Tristan Glatard, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 08. BigBrain dataset and pipeline launching - NeuroHub overview

Bryan L. Caron, NeuroHub, Montreal Neurological Institute, McGill University

Day 1 - 09. Hands-on: CBRAIN portal

Natacha Beck, McGill University, Montreal, Canada

This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

Day 1 - 10. BigBrain as part of the EBRAINS human brain atlas

Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

The EBRAINS multilevel human brain atlas integrates maps that capture different facets of human brain organization into a common framework. It is defined across multiple reference spaces, where BigBrain represents the micrometer level.

Day 1 - 11. Introduction to Atelier3D

Louis Borgeat, Philippe Massicotte, National Research Council of Canada

This tutorial introduces the Atelier3D-MCIN software and utilities, and provide walk troughs of different annotations and mapping applications for the big brain. Atelier3D is a Windows and Linux-based software platform that provides powerful processing and visualization tools for the analysis of very large volume and surface datasets, and this version has been specifically adapted to support 3D annotation, segmentation and 3D surface extraction in the big brain in support of different use cases in McGill and Juelich.

Day 1 - 12. Atelier3D: User perspective

Andrea Brandtstetter, , Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

This tutorial introduces the Atelier3D-MCIN software and utilities, and provide walk troughs of different annotations and mapping applications for the big brain. Atelier3D is a Windows and Linux-based software platform that provides powerful processing and visualization tools for the analysis of very large volume and surface datasets, and this version has been specifically adapted to support 3D annotation, segmentation and 3D surface extraction in the big brain in support of different use cases in McGill and Juelich.

Day 1 - 13. Atelier3D: Use case and current developments

Mona Omidyeganeh, National Research Council of Canada and McGill Centre for Integrative Neuroscience, McGill University, Canada

This tutorial introduces the Atelier3D-MCIN software and utilities, and provide walk troughs of different annotations and mapping applications for the big brain. Atelier3D is a Windows and Linux-based software platform that provides powerful processing and visualization tools for the analysis of very large volume and surface datasets, and this version has been specifically adapted to support 3D annotation, segmentation and 3D surface extraction in the big brain in support of different use cases in McGill and Juelich.

Day 1 - 14. Wrap-up

Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

Day 2 - 01. The BigBrain Warp

Casey Paquola, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

The BigBrain Warp is a toolbox for multi-modal integration of BigBrain, composed of a centralised repository of BigBrain related transformations and scripts to easily move between histological and MRI spaces. This session introduces the toolbox and presents short tutorials on how to use BigBrain in the context of structural and functional MRI.

Day 2 - 02. VoluBA

Sebastian Bludau, Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

VoluBA ("Volumetric Brain Anchoring") is an online service which allows to upload a high-resolution volume of interest (VOI) to perform interactive anchoring to the BigBrain, without the need of downloading the BigBrain volume to a local machine.

Day 2 - 03. Algorithms for Segmenting the Brain

Thomas Funck, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany

This tutorial gives a brief overview and hands on examples for common techniques that can be used to segment brain images. It starts by looking at simple, but powerful, histogram thresholding, before touching on some common machine learning techniques, ending with a look at neural networks.

Day 2 - 04. The BigBrain Atlas of Cortical Layers

Konrad Wagstyl, Wellcome Centre for Human Neuroimaging, University College London, UK

This tutorial provides examples for how to interact with the laminar atlas of the BigBrain using jupyter notebooks and python. Different exmaples are presented using the segmented BigBrain volume, mesh surfaces and surface-based maps of laminar thickness and intensity, as well as basic tools for visualising the data.

Day 2 - 05. Microdraw

Katja Heuer, CRI Centre de Recherche Interdisciplinaire

Roberto Toro, Department of Neuroscience, Institut Pasteur

High resolution histological data provides a unique perspective on the cellular structure of the brain. Histological data is available for a large number of species, and the possibility of staining for particular aspects of the tissue allows the researcher to formulate an extremely rich range of questions.

Day 2 - 06. Wrap-up

Alan Evans, James McGill Professor of Neurology, Psychiatry, Biomedical Eng., McGill Centre for Integrative Neuroscience, McGill University.