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<!doctype html>
<html>
<head>
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<meta charset="utf-8">
<title>the BigBrain</title>
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<meta name="description" content="This is the website of the BigBrain Project.">
<meta name="keywords" content="Neuro, Brain, Research, Big Data, Science, Medicine">
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</ul>
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<li class="nav-item"><a href="maps-and-models.html">Maps & Models</a></li>
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</ul>
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<!-- intro section -->
<section class="hero tools-services-bg">
<div class="grid-container">
<div class="hero-content-grid">
<div class="hero-content-container">
<h1>BigBrain Tools & Services</h1>
<p>The BigBrain project develops a highly compatible and unified resource across Canadian and European neuroscience IT ecosystems to host high-resolution human brain models and connect them with different neuroinformatics services. We also foster co-development of solutions for viewing and annotating large volumetric data, and improving the cross-continental compatibility of datasets and neuroinformatics APIs</p>
<div class="hero-flex">
<!-- <a href="news.html"><button>read about the history & vision</button></a> -->
<a href="https://bigbrain.humanbrainproject.org/"><button>view data in browser</button></a>
<a href="maps-and-models.html#download"><button>access the dataset</button></a>
</div>
</div>
</div>
</div>
</section>
<div class="clear-all"></div>
<!-- tools section -->
<section class="extra-pad lt-grey-bg">
<div class="section-content lt-grey-bg end">
<h1 class="full-width text-center">Tools</h1>
<h2 id="stickypad" class="full-width text-center">Partner and community developed BigBrain tools</h2>
<div id="tabs">
<ul id="second-nav" class="tabs-list">
<li>
<a href="#tabs-1">
<button data-mh="button">
Visualization and Annotation
</button>
</a>
</li>
<li>
<a href="#tabs-2">
<button data-mh="button">
Neuroinformatics Infrastructure
</button>
</a>
</li>
<li>
<a href="#tabs-3">
<button data-mh="button">
Computing Services
</button>
</a>
</li>
<li>
<a href="#tabs-4">
<button data-mh="button">
Community Contributed Tools
</button>
</a>
</li>
<li>
<a href="#tabs-5">
<button data-mh="button">
Base Infrastructure
</button>
</a>
</li>
<li>
<a href="#tabs-6">
<button data-mh="button">
Supported Standards
</button>
</a>
</li>
</ul>
<a href="" class="anchor" id="tabs-1"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Visualization and Annotation</h2>
<div id="slick-slider-6" class="slider">
<!-- start cards -->
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/display.jpg" class="card-image-square">
<div class="tool-name">Display</div>
<div class="tool-maker"><em>by:</em> David MacDonald et al</div>
<div class="tool-description">Display is designed to visualize and manipulate three dimensional objects, such as human cortical surfaces and sulcal curves.</div>
<a href="http://mcin.ca/technology/visualization/display/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/a3d.jpg" class="card-image-square">
<div class="tool-name">Atelier3D</div>
<div class="tool-maker"><em>by:</em> Louis Borgeat, Philippe Massicotte, et al</div>
<div class="tool-description">Atelier3D is a visualisation and annotation tool from NRC Computer Vision and Graphics</div>
<a href="https://nrc.canada.ca/en/research-development/products-services/technical-advisory-services/computer-vision-graphics" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/hbp-logo.jpg" class="card-image-square">
<div class="tool-name">Human Brain NeHuBa</div>
<div class="tool-maker"><em>by:</em> Various</div>
<div class="tool-description">Tools and visualization application on the HBP website.</div>
<a href="https://interactive-viewer.apps.hbp.eu/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/brainbrowser.png" class="card-image-square">
<div class="tool-name">BrainBrowser</div>
<div class="tool-maker"><em>by:</em> Tarek Sherif et al</div>
<div class="tool-description">BrainBrowser is a set of web-based 3D visualization tools primarily used for viewing neurological data, such as MRI scans. The surface viewer was modified by Natacha Beck and Lindsay B Lewis to handle the BigBrain surfaces created by C Lepage, A Altinkaya, and various contributors.</div>
<a href="http://natacha-beck.github.io/brainbrowser/BrainBrowserSurfaceUI/" class="tool-link">Open in browser <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/microdraw.jpg" class="card-image-square">
<div class="tool-name">MicroDraw</div>
<div class="tool-maker"><em>by:</em> Roberto Toro et al</div>
<div class="tool-description">MicroDraw is a web application to visualise and annotate collaboratively high resolution histology data.</div>
<a href="http://microdraw.pasteur.fr/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
</div>
</div>
<a href="" class="anchor" id="tabs-2"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Neuroinformatics Infrastructure</h2>
<div id="slick-slider-2" class="slider">
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/cbrain.jpg" class="card-image-square">
<div class="tool-name">CBRAIN</div>
<div class="tool-maker"><em>by:</em> CBRAIN team</div>
<div class="tool-description">CBRAIN is an infrastructure that connects researchers and data from all walks of science to high performance and cloud computing in an easy to manage, reproducible, and user-friendly manner.</div>
<a href="http://www.cbrain.ca/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/LORIS-logo-color.png" class="card-image-square">
<div class="tool-name">LORIS</div>
<div class="tool-maker"><em>by:</em> LORIS team</div>
<div class="tool-description">(Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework for storing and processing behavioural, clinical, neuroimaging and genetic data.</div>
<a href="http://loris.ca/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/datalad.png" class="card-image-square">
<div class="tool-name">DataLad</div>
<div class="tool-maker"></div>
<div class="tool-description">When publishing data, merely providing file access is insufficient for a simple reason: data are not static. Released data often (and should!) continue to evolve; file formats can change, bugs will be fixed, new data are added, and derived data needs to be integrated.</div>
<a href="https://www.datalad.org/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/neurohub.png" class="card-image-square">
<div class="tool-name">Neurohub</div>
<div class="tool-maker"></div>
<div class="tool-description">NeuroHub allows access to powerful computational tools for data processing and streamlined systems for secure storage and sharing of multi-disciplinary data.</div>
<a href="https://neurohub.ca/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
</div>
</div>
<a href="" class="anchor" id="tabs-3"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Computing Services</h2>
<div id="slick-slider-3" class="slider">
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/calculquebec.png" class="card-image-square">
<div class="tool-name">Calcul Québec</div>
<div class="tool-maker"></div>
<div class="tool-description">Calcul Québec’s supercomputers, located in various universities, are available to researchers from across Quebec and Canada. Our systems total over 80 000 cores in a variety of configurations.</div>
<a href="https://www.calculquebec.ca/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/computecanada.jpg" class="card-image-square">
<div class="tool-name">Compute Canada</div>
<div class="tool-maker"></div>
<div class="tool-description">High performance computing</div>
<a href="https://www.computecanada.ca/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/jsc.jpg" class="card-image-square">
<div class="tool-name">Juelich Supercomputing Centre</div>
<div class="tool-maker"></div>
<div class="tool-description">The Jülich Supercomputing Centre (JSC) at Forschungszentrum Jülich enables scientists and engineers to solve highly complex, grand challenges in science and engineering within collaborative infrastructures for both supercomputing and grid technologies.</div>
<a href="https://www.gauss-centre.eu/about-us/our-centres/juelich-supercomputing-centre/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
</div>
</div>
<a href="" class="anchor" id="tabs-4"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Community Contributed Tools</h2>
<div id="slick-slider-4" class="slider">
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/featured/featured-1.png" class="card-image-square">
<div class="tool-name">Featured: BigBrain Warp</div>
<div class="tool-maker"><em>date: Apr 01 2021</em></div>
<div class="tool-description">Our featured tool developed by Casey Paquola and Boris Bernhardt.
</div>
<a href="https://bigbrainwarp.readthedocs.io/en/latest/" class="tool-link">go to the project <i class="fas fa-arrow-right"></i></a><br>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/chimera.jpg" class="card-image-square">
<div class="tool-name">The Human Brain in Chimera</div>
<div class="tool-maker"><em>by:</em> Tom Goddard</div>
<div class="tool-description">A tutorial on how to visualize the BigBrain in Chimera using the MINC format.</div>
<a href="https://www.cgl.ucsf.edu/chimera/data/bigbrain-jul2013/bigbrain.html" class="tool-link">Go to tool <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/brainbox.png" class="card-image-square">
<div class="tool-name">The BrainBox</div>
<div class="tool-maker"><em>by:</em> Various</div>
<div class="tool-description">BrainBox allows you to visualise, segment and annotate collaboratively any brain MRI dataset available online.</div>
<a href="https://brainbox.pasteur.fr/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/virtualbrain.jpg" class="card-image-square">
<div class="tool-name">The Virtual Brain</div>
<div class="tool-maker"><em>by:</em> Viktor Jirsa et al</div>
<div class="tool-description">A multiscale integration and simulation platform for brain network computation.</div>
<a href="https://www.thevirtualbrain.org/tvb/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
</div>
</div>
<a href="" class="anchor" id="tabs-5"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Base Infrastructure</h2>
<div id="slick-slider-5" class="slider">
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/huron.png" class="card-image-square">
<div class="tool-name">Huron Scanners</div>
<div class="tool-maker"></div>
<div class="tool-description">High resolution scanners from Huron Digital Pathology.</div>
<a href="http://www.hurondigitalpathology.com/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
</div>
</div>
<a href="" class="anchor" id="tabs-6"></a>
<div class="big-spacer">
<h2 class="full-width text-center">Supported Standards</h2>
<div id="slick-slider-7" class="slider">
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/incf.png" class="card-image-square">
<div class="tool-name">International Neuroinformatics Coordinating Facility</div>
<div class="tool-maker"></div>
<div class="tool-description">The mission of the International Neuroinformatics Coordinating Facility (INCF) is to develop, evaluate, and endorse standards and best practices that embrace the principles of Open, FAIR, and Citable neuroscience.</div>
<a href="https://www.incf.org/" class="tool-link">Go to website <i class="fas fa-arrow-right"></i></a>
</div>
</div>
<div class="slider-card-holder">
<div class="frontpage-card" data-mh="toolcard">
<img src="images/tools/boutiques.jpg" class="card-image-square">
<div class="tool-name">Boutiques</div>
<div class="tool-maker"><em>by:</em> Tristan Glatard et al</div>
<div class="tool-description">A cross-platform descriptive command-line framework for applications.</div>
<a href="https://boutiques.github.io/" class="tool-link">Open in Github <i class="fas fa-arrow-right"></i></a>
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<blockquote class="quote-holder">
<img class="quote-image" src="images/icon-aquisition.png">
<p class="quote-text">An exciting new opportunity.</p>
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<div class="section-content flex">
<a href="https://www.fz-juelich.de/">
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<a href="https://mcgill.ca/">
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<p class="center" style="color: #fff;">For information please email us at <a href="mailto:[email protected]">[email protected]</a>
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