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<!doctype html>
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<title>the BigBrain</title>
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<h1>Vision and Mission</h1>
<p>Neuroimaging methods rely on accurate brain models as ground truth to develop reliable approaches for probing the brain. Researchers in brain simulation and AI have a growing need for detailed descriptions of the internal organisation of brain regions in terms of local morphology, cell densities, or connectivity. Currently established computer-based 3D neuroimaging tools cannot reproduce the anatomical details available from freshly cut brains, particularly for very convoluted cortical regions and in the subcortical areas. With the advent of the BigBrain - a human post-mortem brain that has been sectioned, stained for cell bodies, scanned at very high resolution, and then digitally reconstructed in 3D (Amunts, Evans et al. 2013), we believe that there will be improvement in the precision and quality of neuroimaging support for qualitative and quantitative investigation of the brain. We aim to extend this model by further increasing its resolution and integrating multimodal data, working closely with the neuroimaging, brain modelling, and AI communities to unleash its potential for research. To enable collaboration, we build a transcontinental data sharing and computing platform in close interaction with the European "Human Brain Project" and the Canadian “Healthy Brains, Healthy Lives” program.</p>
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<h2 class="small-spacer">BigBrain Goals</h2>
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<span class="flex-center">Building a highly detailed multimodal atlas</span>
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Building a highly detailed multimodal atlas<br><br>
By developing novel AI-based methods for analyzing high-resolution image data, we create highly detailed maps of brain areas, cortical layers, and subcortical structures for our microscopic brain models. We complement the cytoarchitectonic model by modalities that cover fibre- and chemoarchitecture, working towards a multimodal characterization of the human brain at the microscopic scale. Furthermore, we work towards a model with a resolution in 1 micron range, which resolves individual neuronal cell bodies.</span>
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<span class="flex-center">Build on the existing 3D BigBrain as a microscopic reference template</span>
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Build on the existing 3D BigBrain as a microscopic reference template<br><br>
We integrate our ongoing developments with the original BigBrain model (Amunts, Evans et al. 2013) in order to foster a common microscopic reference template. This includes efforts on careful spatial registration across subjects and modalities, and propagation of maps of brain regions. </span>
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<span class="flex-center">Building a distributed platform for big neuroscience data</span>
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Building a distributed platform for big neuroscience data<br><br>
By increasing the resolution to the level of individual neuronal cell bodies, the size of whole brain models reaches the Petabyte scale. To address such Big Data challenge, we establish specific workflows for distributed data management and processing, and tools for remote visualization and annotation of 2D and 3D data. This also requires standardization efforts for data and metadata formats. We align these infrastructure development efforts with the developments of the Human Brain Project and the HBHL program to maximize compatibility with the international initiatives.</span>
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<span class="flex-center">AI link to data science and brain inspired computing</span>
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AI link to data science and brain inspired computing<br><br>
The BigBrain project is entangled with AI research in two fundamental ways - by developing novel image analysis methods based on Machine and Deep Learning, and by contributing knowledge about the microstructural organization of biological neural networks in the brain. The project initiates early cooperation with researchers in brain inspired AI and computing to incorporate information about the human brain into the design of artificial systems.</span>
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<span class="flex-center">Virtual BigBrain and simulation platform</span>
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Virtual BigBrain and simulation platform<br><br>
The VirtualBrain (TVB) uses empirical knowledge of brain structure to constrain models that simulate network dynamics, which in turn can be validated with experimental observations of brain function. Complementing related work in the Human Brain Project, we support the development of TVB models with increased spatial resolution and regional heterogeneity by informing them with microscopic resolution data, and evaluating optimized software and hardware environments for the CBRAIN platform.</span>
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<span class="flex-center">Open Community Resource</span>
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Open Community Resource<br><br>
The BigBrain Project continues to build an open resource and a lively scientific community within a collaborative research and training environment. We will share our datasets and tools through the platform, aim to integrate them with the EBRAINS and CBRAIN ecosystems, and engage with the BigBrain user and contributor community through open project meetings, workshops, and online services.</span>
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<h1 class="text-center spacer">History of BigBrain</h1>
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<h2>1. What is the BigBrain</h2>
<p>BigBrain is a freely accessible high-resolution 3D digital model of the human brain, released in June 2013 by a team of researchers at the Montreal Neurological Institute (Canada) and the Forschungszentrum Jülich (Germany). The isotropic 3D spatial resolution of the BigBrain atlas is 20 µm, much finer than other models. In 2014, BigBrain was cited in the <a href="http://www.technologyreview.com/featuredstory/526501/brain-mapping/">Top 10 MIT Technology Review</a>. Since then, it is continuously enriched by detailed maps of cortical areas and layers as well as subcortical regions. It became the basis of many neuroscientific studies.</p>
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<p class="caption">Digital rendering with CIVET<br>
<a href="http://mcin-cnim.ca/wp-content/uploads/2017/08/RBIQ2016BigBrain.png">OHBM poster from 2016</a>
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<h2>2. Acquisition: Source brain</h2>
<p>The 3D model was created from the brain of an unidentified 65-year-old man who died with no known brain pathology. The postmortem brain, which was obtained in accordance with ethical requirements of the University of Düsseldorf, was first scanned using an MRI machine, then embedded in paraffin.</p>
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<p class="caption">Body donor gave written informed consent for the general use of postmortem tissue used in this study for aims of research and education. The usage is covered by a vote of the ethics committee of the medical faculty of the Heinrich Heine, University Düsseldorf (#4863).</p>
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<p class="caption">A paraffin embedded brain was cut into 7404 histological sections, each 20 micrometers thick, using a microtome.<br> Copyright: Amunts, Zilles, Evans et al. </p>
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<h2>2. Acquisition, histological processing, and digitization at 20 μm</h2>
<p>The 3D model was created from the brain of an 65-year-old body donor. The postmortem brain was obtained in accordance with ethical requirements of the University of Düsseldorf. It was fixed in formalin, and imaged in 2003 using a MR scanner. In 2005, it was cut into 7,404 sections 20 µm thick using a large-scale microtome. The brain sections were placed on glass slides and stained for cell bodies using the Merker method, resulting in darkly stained neurons and light neuropile, i.e. the space in between neurons filled with the branches of the cells and synapses. The stained sections were scanned and digitized using a flatbed scanner at 2400dpi (10 µm), creating a one Terabyte raw record. The acquisition process (wet work + scanning) took about 1,000 hours of labor.</p>
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<h2>3. Manual repairing of tissue artefacts in the images </h2>
<p>The resulting digital images were carefully processed by a team of operators to identify and manually fix artifacts such as tears and folds, which arise inevitably during histological processing. The manual repair process was complemented by automated repairs, carefully blending information from neighbouring sections to replace missing pieces of brain tissue where required.</p>
</div>
</div>
</div>
<div class="testimonial">
<div class="col-2 flex-center">
<a href="images/history-aquisition.png" data-lightbox="bbstory">
<img src="images/history-aquisition.png">
</a>
<p class="caption">Digital rendering with CIVET<br>
<a href="http://mcin-cnim.ca/wp-content/uploads/2017/08/RBIQ2016BigBrain.png">OHBM poster from 2016</a>
</p>
</div>
<div class="col-2">
<div class="text-box">
<h2>4. 3D reconstruction using image processing with HPC</h2>
<p>The corrected digital sections were nonlinearly registered to the postmortem MRI in an iterative process, and reassembled into a consistent 3D computer model with a spatial isotropic 3D resolution of 20 µm. The aligned images were optically balanced to remove colouring artifacts from staining. Dealing with more than 7000 images, this was a highly complex and compute intensive process which would not have been possible without supercomputers. Including all manual work, the 3D reconstruction took five years to complete.</p>
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</div>
</div>
<div class="testimonial">
<div class="col-2 flex-center">
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<img src="images/neuroglancer.png">
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<a href="images/a3d.png" data-lightbox="bbstory">
<img src="images/a3d.png">
</a>
</div>
<div class="col-2">
<div class="text-box">
<h2>5. Rendering and annotating the BigBrain </h2>
<p>Standard tools for volumetric image rendering and annotation were not applicable to the BigBrain due to its size: A Terabyte of image date does not fit into a typical computer’s working memory. Specific software had to be developed which provides very efficient loading and rendering of the image data to visualize the BigBrain and allow smooth interactions and annotations in 3D space. The Atelier3D software developed by the National Research Council Canada (NRC) is one of the few available tools that were able at that time to render and interactively annotate such huge image volumes, and had been specifically adjusted for brain navigation and mapping.<!-- <a href="https://bigbrain.humanbrainproject.eu ">https://bigbrain.humanbrainproject.eu</a> --></p>
</div>
</div>
</div>
<div class="testimonial">
<div class="col-2 flex-center">
<a href="images/history-analysis.png" data-lightbox="bbstory">
<img src="images/history-analysis.png">
</a>
</div>
<div class="col-2">
<div class="text-box">
<h2>6. Analysis: Mapping of the BigBrain</h2>
<p>We have applied different approaches to map cortical areas and subcortical nuclei in the BigBrain. For the cerebral cortex, we applied image analysis and statistical tools to identify borders between areas (Schleicher et al., 2005), while nuclei were manually delineated. Most recently, automatic methods derived from artificial intelligence (machine learning and deep learning) were applied map brain areas (Spitzer et al.), and to extract cortical layers or count groups of cells (Wagstyl et al.). Check out recent work on our <a href="https://3design.github.io/news.html">news feed!</a></p>
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</div>
</div>
<div class="testimonial">
<div class="col-2 flex-center">
<a href="images/a3d.png" data-lightbox="bbstory">
<img src="images/a3d.png">
</a>
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<div class="col-2">
<div class="text-box">
<h2>7. Dissemination: Sharing the atlas with the world</h2>
<p>The BigBrain image datasets are currently hosted by the project on an <a href="https://ftp.bigbrainproject.org/">ftp server</a>. The model has been integrated as a core reference space of the multilevel human brain atlas of the <a href="https://ebrains.eu/services/atlases/brain-atlases">Human Brain Project</a>. In the future, data sharing will be offered through a fully versioned online system developed within the framework of <a href="hiball.html">HIBALL</a>. In Summer 2017 the first version of the Human Brain Project’s web-based 3D atlas viewer was released, building on Google’s open source project Neuroglancer. It is capable of displaying very large brain volumes, including oblique slicing, a whole brain overview, surface meshes, and maps. It enables navigating the BigBrain in 3D, exploring the growing set of highly detailed maps for cortical layers and cytoarchitectonic areas, and finding related neuroscience data. BigBrain can be explored in the viewer at <a href="https://bigbrain.humanbrainproject.eu">Human Brain Project website.</a> </p>
</div>
</div>
</div>
</div>
</div>
</section>
<!-- publications section -->
<section class="lt-grey-bg">
<div class="section-content flex lt-grey-bg">
<h1 class="full-width text-center">BigBrain Featured</h1>
<h2 class="full-width text-center">Major publications featuring the dataset</h2>
<div class="col-2 wide-card">
<div class="col-2">
<img src="images/science_cover.gif" class="BigBrainPic" data-mh="card-pic">
</div>
<div class="col-2">
<div class="text-box">
<div class="small-spacer" data-mh="card-details">
<h1>Science Magazine</h1>
<h2>BigBrain: An Ultrahigh-Resolution 3D Human Brain Model</h2>
<p>The original publication of the BigBrain</p>
</div>
<a href="https://science.sciencemag.org/content/340/6139/1472"><button class="float-right">read the full article</button></a>
</div>
</div>
</div>
<div class="col-2 wide-card">
<div class="col-2 ">
<img src="images/mit-magazine.jpg" class="BigBrainPic" data-mh="card-pic">
</div>
<div class="col-2">
<div class="text-box">
<div class="small-spacer" data-mh="card-details">
<h1>MIT Technology Review</h1>
<h2>One of the Top 10 Breakthroughs of 2014 </h2>
<p>MIT Technology Review listed the BigBrain as 1 of the Top 10 Breakthroughs of 2014.</p>
</div>
<a href="http://www.technologyreview.com/featuredstory/526501/brain-mapping/"><button class="float-right">read the full article</button></a>
</div>
</div>
</div>
</div>
</section>
<div class="clear-all"></div>
<!-- team section -->
<section>
<div class="section-content no-side-pad max100">
<h1 class="full-width text-center">BigBrain team</h1>
<h2 class="full-width text-center">The people from the original project</h2>
<div class="mosaic">
<img src="images/profile-katrin-amunts.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small"><a href="https://www.fz-juelich.de/profile/amunts_k">Katrin Amunts</a></div>
<div class="card-jobtitle">Director, Institute Structural and functional organisation of the brain (INM-1)</div>
<a href="https://www.fz-juelich.de/en/inm/inm-1" class="wordbreak">Forschungszentrum Jülich</a>
<br>
<div class="card-jobtitle">Director, C. and O. Vogt-Institute of Brain Research</div>
<a href="https://www.uniklinik-duesseldorf.de/patienten-besucher/klinikeninstitutezentren/c-u-o-vogt-institut-fuer-hirnforschung">Universitätsklinikum Düsseldorf</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/profile-temp2.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name mcgill-small">Claude Lepage</div>
<div class="card-jobtitle">Development and programming of image-processing tools for 3D reconstruction/alignment and automatic repair pipelines, manual repairs, registration, quality control and documentation</div>
<a href="http://mcin.ca">McGill Centre for Integrative Neuroscience</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-louis.jpg" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name other-small">Louis Borgeat</div>
<div class="card-jobtitle">Volume data modeling and integration, development of the Atelier3D remote visualization and analysis tools</div>
<a href="https://nrc.canada.ca/">National Research Council of Canada</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/profile-temp2.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small"><a href="https://www.fz-juelich.de/profile/mohlberg_h">Hartmut Mohlberg</a></div>
Institute structural and functional organisation of the brain (INM-1)<br><br>
<a href="https://www.fz-juelich.de/en/inm/inm-1">Forschungszentrum Jülich</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-dickscheid.jpg" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small"><a href="https://www.fz-juelich.de/profile/dickscheid_t">Timo Dickscheid</div>
Institute structural and functional organisation of the brain (INM-1)</a><br><br>
<a href="https://www.fz-juelich.de/en/inm/inm-1">Forschungszentrum Jülich</a>
</div>
</div>
<div class=" mosaic">
<img src="images/team/team-marc.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name mcgill-small">Marc-Étienne Rousseau </div>
<div class="card-jobtitle">Computing platform manager</div>
<a href="http://mcin.ca">McGill Centre for Integrative Neuroscience</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-bludau.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small"><a href=" https://www.fz-juelich.de/profile/bludau_s">Sebastian Bludau</a></div>
Institute structural and functional organisation of the brain (INM-1)<br><br>
<a href="https://www.fz-juelich.de/en/inm/inm-1">Forschungszentrum Jülich</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-bazin.jpg" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name other-small">Pierre-Louis Bazin</div>
<div class="card-jobtitle">Senior Onderzoeker</div>
<a href="https://herseninstituut.nl/over-ons/de-organisatie/medewerkers/pierre-louis-bazin/">Herseninstituut</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-llewis.jpg" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name mcgill-small">Lindsay B. Lewis</div>
<div class="card-jobtitle">Manual repairs, quality control and documentation</div>
<a href="http://mcin.ca">McGill Centre for Integrative Neuroscience</a>
</div>
</div>
<div class=" mosaic">
<img src="images/team/team-oros-peusquens.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small">Ana-Maria Oros-Peusquens</div>
<div class="card-jobtitle">Institute structural and functional organisation of the brain (INM-1)</div>
<a href="https://www.fz-juelich.de/en/inm/inm-1" class="wordbreak">Forschungszentrum Jülich</a>
</div>
</div>
<div class=" mosaic">
<img src="images/team/team-shah.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small">Nadim J. Shah</div>
<div class="card-jobtitle">Director of the Institute Medical Imaging Physics (INM-4)</div>
<a href="https://www.fz-juelich.de/en/inm/inm-4" class="wordbreak">Forschungszentrum Jülich</a>
</div>
</div>
<div class="mosaic">
<img src="images/team/team-lippert.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small">Thomas Lippert</div>
<div class="card-jobtitle">Director of the Institute for Advanced Simulation, Head of Jülich Supercomputing Centre</div>
<a href="https://www.fz-juelich.de/en/ias/jsc" class="wordbreak">Forschungszentrum Jülich</a>
</div>
</div>
<div class=" mosaic">
<img src="images/dr-zilles.jpg" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name julich-small"> Karl Zilles</div>
<div class="card-jobtitle">Institute structural and functional organisation of the brain (INM-1), Forschungszentrum Jülich</div>
<a href="https://www.fz-juelich.de/inm/inm-1/EN/Home/home_node.html" class="wordbreak">Forschungszentrum Jülich</a>
<div class="card-jobtitle">former Director of the Institute of Neuroscience and Medicine</div>
<div class="card-jobtitle">former director of the C. and O. Vogt-Institute of Brain Research</div>
</div>
</div>
<div class="mosaic">
<img src="images/profile-alan-evans.png" class="">
<div class="mosaic-overlay">
<div class="mosiac-overlay-name mcgill-small">Alan Evans</div>
<div class="card-jobtitle">James McGill Professor of Neurology, Psychiatry, Biomedical Eng.</div>
<a href="https://mcgill.ca">McGill University</a>
<a href="http://mcin.ca">mcin.ca</a>
</div>
</div>
<div class="clear-all spacer"></div>
<!-- additional team list -->
<ul class="contributors-list">
<li class="contributor mcgill-small">
Reza Adalat, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor julich-small">
René Bergs, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Ursula Blohm, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor mcgill-small">
Samir Das, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor julich-small">
Franziska Henke, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
René Hübbers, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Timo Hütz, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Florian Janetzko, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor other-small">
Andrew Janke, <a href="https://cai.centre.uq.edu.au/" class="">Center for Advanced Imaging, University of Queensland</a>
</li>
<li class="contributor mcgill-small">
Nicolas Kassis, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor julich-small">
Melanie Kleiner, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Ferdag Kocaer, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor mcgill-small">
Dave MacFarlane, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor other-small">
Philippe Massicotte, <a href="https://nrc.canada.ca/" class="">National Research Council of Canada</a>
</li>
<li class="contributor julich-small">
Patricia Morosan, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Katja Morstadt, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor mcgill-small">
Mia Petkova, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor julich-small">
Uwe Pietrzyk, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor julich-small">
Julia Reckfort, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor mcgill-small">
Pierre Rioux, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor julich-small">
Martin Schober, <a href="https://www.fz-juelich.de" class="">Forschungszentrum Jülich</a>
</li>
<li class="contributor mcgill-small">
Tarek Sherif, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor mcgill-small">
Jordan Sterling, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
<li class="contributor mcgill-small">
Robert Vincent, <a href="http://mcin.ca/" class="">McGill Centre for Integrative Neuroscience</a>
</li>
</ul>
</div>
</section>
<!-- faq section -->
<section class="lt-grey-bg">
<a class="anchor" id="FAQ"></a>
<div class="section-content flex lt-grey-bg">
<h1 class="full-width text-center">BigBrain FAQ</h1>
<h2 class="full-width text-center">Frequently asked questions about the BigBrain</h2>
<!-- accordian -->
<div class="accordian">
<ul>
<li>
<h3 class="title">
<span class="fa fa-plus"></span>
<span class="faq-q">Q: </span>
<p class="question">What is the BigBrain</p>
</h3>
<p class="answer"><span class="faq-q">A: </span>The BigBrain is the brain of a 65yo man with no neurological or psychiatric diseases in clinical records at time of death. The brain was embedded in paraffin and sectioned in 7404 coronal histological sections (20 microns), stained for cell bodies. The BigBrain is the digitized 3D reconstruction of the high-resolution histological sections (20 microns isotropic).</p>
</li>
<li>
<h3 class="title">
<span class="fa fa-plus"></span>
<span class="faq-q">Q: </span>
<a class="anchor" id="citation"></a>
<p class="question">How to Cite</p>
</h3>
<p class="answer"><span class="faq-q">A: </span>When referring to the BigBrain Project or using the data, please cite the original Science 2013 publication:<br><br>Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau M-É, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC. BigBrain: An ultrahigh-resolution 3D human brain model. Science. 2013; 340(6139):1472-1475. doi: 10.1126/science.1235381. PMID: 23788795.</p>
</li>
<li>
<h3 class="title">
<span class="fa fa-plus"></span>
<span class="faq-q">Q: </span>
<a class="anchor" id="citation"></a>
<p class="question">What is the ethics statement for the source brain</p>
</h3>
<p class="answer"><span class="faq-q">A: </span>Body donor gave written informed consent for the general use of postmortem tissue used in this study for aims of research and education. The usage is covered by a vote of the Ethics Committee of the Faculty of Medicine at Heinrich Heine University Düsseldorf (#4863).</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">What volumes of BigBrain are available?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>The
<a href="https://bigbrain.loris.ca/main.php?test_name=brainvolumes&release=2015">volumes</a>
are represented in either stereotaxic space (MNI-ICBM152 or MNI-ADNI) or in native histological space. The stereotaxic registration is not perfect but it is very good. The templates for registration (ICBM152 and ADNI) are made available in those tables. The BigBrain volumes are offered at 100, 200, 300, 400 microns isotropic in both MINC (.mnc) and NIfTI (.nii) formats.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">Why is the aligned BigBrain showing such strong asymmetry?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>The asymmetry results from aligning the histology sections to the MRI of the brain after it was extracted from the skull and set in formalin. We do not have a post-mortem MRI of the undistorted brain inside the head.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">The intensities are wrong in the NIfTI volumes. How can I view them correctly?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>There was a problem with the initial data conversion to NIfTI format. The NIfTI volumes have been replaced on Sept 3, 2013. You will have to download the new volumes to view them in FSLView, MRIcron or AFNI tools.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">Where are the 100um NIfTI volumes?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>The 100um NIfTI volumes could not be created initially because of file size limitations of the data converter. They are now available.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">How can I download the MINC volumes? The files appear incomplete.</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>Volumes in MINC and NIfTI can be downloaded from
<a href="https://ftp.bigbrainproject.org/bigbrain-ftp/BigBrainRelease.2015/3D_Volumes/">the ftp site</a> or from <a href="https://bigbrain.loris.ca/main.php?test_name=brainvolumes&release=2015">LORIS</a>. Your browser may be limiting the maximum size of the file to transfer. This may be problematic for the 100-micron volumes.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">How can I view the MINC volumes?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>MINC is an imaging format developed at the MNI. To obtain binaries (mostly Linux and OSX) of the MINC tools, download the <a href="http://bic-mni.github.io/">MINC Tool Kit</a>. The image viewers are called register and Display.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">How do I view the volumes online?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>You can explore the high resolution human brain model online in the <a href="https://atlases.ebrains.eu/viewer/#/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:a1655b99-82f1-420f-a3c2-fe80fd4c8588/p:juelich:iav:atlas:v1.0.0:4/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..gIW~.10AwC.B1KK~..1LSm">EBRAINS siibra explorer</a>. </p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">How can I view the surfaces?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>The MNI-OBJ surfaces are viewable in a web-based fashion using <a href="https://brainbrowser.cbrain.mcgill.ca/">BrainBrowser</a> or <a href="https://natacha-beck.github.io/brainbrowser/BrainBrowserSurfaceUI/">BigBrainBrowser</a>. The surfaces are also available in various other formats (STL, gii, WaveFront-OBJ, etc) for viewing with other standard tools in the field.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">Is there an MRI of the BigBrain?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>Yes, there is an <a href="https://ftp.bigbrainproject.org/bigbrain-ftp/Raw_Data/MRI/">MRI</a> of the fixed brain (removed from skull) at an isotropic voxel size resolution of 0.444mm. Note that this MRI is in "processing space" with y-z axes flipped.</p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">How can I view the volumes as in the BigBrain videos?</p>
<span class="fa fa-plus"></span>
</h3>
<p class="answer"><span class="faq-q">A: </span>The bigbrain videos were created using Atelier3D, a licensed software which is currently not distributed. The volume read in Atelier3D is at 20-micron isotropic, which is too big for file transfers. This is why reduced volumes at 100, 200, 300, 400 microns have been created. You can explore the BigBrain online in the
<a href="https://atlases.ebrains.eu/viewer/#/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:a1655b99-82f1-420f-a3c2-fe80fd4c8588/p:juelich:iav:atlas:v1.0.0:4/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..gIW~.10AwC.B1KK~..1LSm">EBRAINS siibra explorer</a>. </p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">Is there sound to the BigBrain videos?</p>
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</h3>
<p class="answer"><span class="faq-q">A: </span>No </p>
</li>
<li>
<h3 class="title">
<span class="faq-q">Q: </span>
<p class="question">Is there a way to mass-download the data files?</p>
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</h3>
<p class="answer"><span class="faq-q">A: </span>Yes. As of March 12th, 2014, all sections and volumes are available on an <a href="https://ftp.bigbrainproject.org/bigbrain-ftp/">anonymous FTP server</a> located at the same address as this site. We recommend connecting to the FTP server using a command line or GUI client (e.g., <a href=" https://filezilla-project.org">Filezilla</a>, but not a web browser).</p>
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