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<h1 class="full-width text-center">HIBALL Winter School 2021</h1>
<!-- <h2 class="full-width text-center">You will be redirected to the official events page in <span id="time">00:42</span> seconds.</h2> -->
<!-- <meta http-equiv = "refresh" content = "42; url = https://hifis-events.hzdr.de/event/37/" /> -->
<p class="center">On February 3-4, 2021, we held our first winter school
around the BigBrain and related datasets and tools. Lectures were given over two half days, and there were practical hands-on sessions. </p>
<p class="center"><em>Scroll down to watch the recordings of the event.</a></em></p>
<div class="hero-logos">
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</section>
<section>
<div class="section-content">
<h2 class="full-width text-center">HIBALL Winter School 2021</h2>
<p>In February 2021 we held the first HIBALL Winter School, which gained a lot of interest. The courses offered introductions and practical hands-on sessions focusing on the BigBrain, related datasets and tools covering IT-Infrastructure, image analysis, visualization and annotation.</p>
<p>With the teaching events of the BigBrain project, we reach out to the thriving community of users and developers which has emerged around the BigBrain. We particularly invite young researchers to join the discussion and become part of the BigBrain community. If you would like to contribute, come join our ongoing conversation on the <a href="https://forum.bigbrainproject.org/">BigBrainProject Forum</a>.</p>
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</section>
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<h2 class="full-width text-center">Participants</h2>
<table class="overview">
<tbody>
<tr>
<td>170+ Registrants</td>
<td>20 Countries</td>
<td>90+ Joining Us Live</td>
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<td class="tg-0lax">Canada</td>
<td class="tg-lqy6">61</td>
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<td class="tg-0lax">Germany</td>
<td class="tg-lqy6">50</td>
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<td class="tg-0lax">India</td>
<td class="tg-lqy6">8</td>
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<td class="tg-0lax">United States</td>
<td class="tg-lqy6">8</td>
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<td class="tg-0lax">United Kingdom</td>
<td class="tg-lqy6">7</td>
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<td class="tg-0lax">China</td>
<td class="tg-lqy6">5</td>
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<td class="tg-0lax">France</td>
<td class="tg-lqy6">3</td>
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<td class="tg-0lax">Netherlands</td>
<td class="tg-lqy6">3</td>
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<td class="tg-0lax">Croatia </td>
<td class="tg-lqy6">2</td>
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<td class="tg-lqy6">2</td>
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<td class="tg-0lax">Spain </td>
<td class="tg-lqy6">2</td>
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<td class="tg-0lax">Switzerland</td>
<td class="tg-lqy6">2</td>
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<td class="tg-0lax">Turkey</td>
<td class="tg-lqy6">2</td>
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<td class="tg-0lax">Australia & Finland</td>
<td class="tg-lqy6">2</td>
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</section>
<!-- videos -->
<section class="med-grey-bg">
<div class="section-content end">
<h2 class="full-width text-center">Program and material <br>
<a href="https://hifis-events.hzdr.de/event/37/">Click here to see the schedule page</a></h2>
<div class="hiballlaunch-card">
<div class="hiballlaunch-vid col-4">
<iframe width="530" height="315" src="https://www.youtube.com/embed/AehFnRa6Ob8" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/AehFnRa6Ob8">Day 1 - 01. Opening Address</a></h3>
<p>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</p>
<!-- <a href="" class="hiballlaunch-button"><button>material</button></a> -->
</div>
</div>
<div class="hiballlaunch-card">
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<iframe width="560" height="315" src="https://www.youtube.com/embed/bTNQCJbYDLE" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/bTNQCJbYDLE">Day 1 - 02. BigBrain anatomy for beginners</a></h3>
<p>Nicola Palomero-Gallagher, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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. </p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Dickscheid.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/djKJpObgkbo" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/djKJpObgkbo">Day 1 - 03. Joint infrastructure for BigBrain</a></h3>
<p>Petur Helgi Einarsson, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Germany, and School of Engineering and Natural Sciences of the University of Iceland</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-vanAlbada.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/hsqYPFYc6d4" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/hsqYPFYc6d4">Day 1 - 04. Short introduction to DataLad and Jülich activities </a></h3>
<p>Morris Riedel, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Germany, and School of Engineering and Natural Sciences of the University of Iceland</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Wagstyl.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/RhB5YVcH8Zo" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
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<h3><a href="https://youtu.be/RhB5YVcH8Zo">Day 1 - 05. Hands-on: BigBrain data processing with CBRAIN and DataLad </a></h3>
<p>Tristan Glatard, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Paquola.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/R6ZWCUWuCbg" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
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<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/R6ZWCUWuCbg">Day 1 - 06. Hands-on: Processing BigBrain datasets with Boutiques</a></h3>
<p>Valérie Hayot-Sasson, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-DeKraker.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/aLvAEBHj_KM" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
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<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/aLvAEBHj_KM">Day 1 - 07. Hands-on: Contributing datasets to archives using DataLad</a></h3>
<p>Tristan Glatard, Big Data Infrastructures for Neuroinformatics Lab, Department of Computer Science and Software Engineering (CSSE), Concordia University, Montreal, Canada</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Funck.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/slATyyZEqJ4" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/slATyyZEqJ4">Day 1 - 08. BigBrain dataset and pipeline launching - NeuroHub overview </a></h3>
<p>Bryan L. Caron, NeuroHub, Montreal Neurological Institute, McGill University</p>
<!-- <p>Institut de Neurosciences des Systèmes, Marseille</p> -->
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Wang.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<div class="hiballlaunch-description col-3">
<h3><a href="https://youtu.be/fNc1t_2IlkI">Day 1 - 09. Hands-on: CBRAIN portal</a></h3>
<p>Natacha Beck, McGill University, Montreal, Canada</p>
<p>This tutorial provides an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.</p>
<!-- <a href="docs/4th-bb-workshop/20-06-26-BigBrainWorkshop-Wang.pdf" class="hiballlaunch-button"><button>PDF of Slides</button></a> -->
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<h3><a href="https://youtu.be/5MWYtDF7Vm0">Day 1 - 10. BigBrain as part of the EBRAINS human brain atlas</a></h3>
<p>Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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. </p>
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<h3><a href="https://youtu.be/jRp-qASUdcg">Day 1 - 11. Introduction to Atelier3D</a></h3>
<p>Louis Borgeat, Philippe Massicotte, National Research Council of Canada</p>
<p>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. </p>
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<h3><a href="https://youtu.be/ru0-OhSS7Nc">Day 1 - 12. Atelier3D: User perspective</a></h3>
<p>Andrea Brandtstetter, , Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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. </p>
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<h3><a href="https://youtu.be/-GjBZ7bFZZA">Day 1 - 13. Atelier3D: Use case and current developments</a></h3>
<p>Mona Omidyeganeh, National Research Council of Canada and McGill Centre for Integrative Neuroscience, McGill University, Canada</p>
<p>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. </p>
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<h3><a href="https://youtu.be/meuTgsT0Fuw">Day 1 - 14. Wrap-up</a></h3>
<p>Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
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<h3><a href="https://youtu.be/Stg_R63GyVY">Day 2 - 01. The BigBrain Warp</a></h3>
<p>Casey Paquola, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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.</p>
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<h3><a href="https://youtu.be/l_7ILe6_2Cs">Day 2 - 02. VoluBA</a></h3>
<p>Sebastian Bludau, Timo Dickscheid, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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.</p>
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<h3><a href="https://youtu.be/6N_M9d4EwBE">Day 2 - 03. Algorithms for Segmenting the Brain</a></h3>
<p>Thomas Funck, Institute of Neuroscience and Medicine, Structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich, Germany</p>
<p>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.</p>
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<h3><a href="https://youtu.be/kcJ7psBkp_A">Day 2 - 04. The BigBrain Atlas of Cortical Layers</a></h3>
<p>Konrad Wagstyl, Wellcome Centre for Human Neuroimaging, University College London, UK</p>
<p>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.</p>
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<h3><a href="https://youtu.be/ZTPuQ0HDgoo">Day 2 - 05. Microdraw</a></h3>
<p>Katja Heuer, CRI Centre de Recherche Interdisciplinaire</p>
<p>Roberto Toro, Department of Neuroscience, Institut Pasteur</p>
<p>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.</p>
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<h3><a href="https://youtu.be/-w7kh63KGB8">Day 2 - 06. Wrap-up</a></h3>
<p>Alan Evans, James McGill Professor of Neurology, Psychiatry, Biomedical Eng., McGill Centre for Integrative Neuroscience, McGill University.</p>
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<p class="center">For information please email us at <a href="mailto:[email protected]">[email protected]</a></p>
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