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Big_brain.html
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Big Brain</title>
<meta name="description" content="A framework for easily creating beautiful presentations using HTML">
<meta name="author" content="Hakim El Hattab">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<!-- The important Javascript libraries -->
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/black.css" id="theme">
<!-- Code syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<!-- MNI ecosystem menu/summary-->
<section>
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<!-- MNI PAPER -->
<section data-transition="fade">
<a href="https://www.researchgate.net/publication/281780543_The_MNI_data-sharing_and_processing_ecosystem" target="_blank"><img src="images/MNI_ecosystem_paper.png" width="90%"></a>
</section>
<section id="fragments">
<h2><font color="12a3d8">What’s involved?</font></h2>
<p>
<span class="fragment">Longitudinal Acquisition, Storage and Curation, </span>
<span class="fragment"><font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, </span>
<span class="fragment">Security, Privacy, Ethics, APIs, </span>
<span class="fragment">Validation, Quality Control, Protocol Checking, </span>
<span class="fragment">Preprocessing, Analysis, HPC, </span>
<span class="fragment">Provenance, Ontological Standarization, <font color="f27c30">Data Harmonization</font>, </span>
<span class="fragment">Upgrades, Maintenance, Bug Fixes, </span>
<span class="fragment">User Interface, Javascript, Bootstrap,</span>
<span class="fragment">Tracking, <font color="f27c30">Extensibility</font>, </span>
<span class="fragment">Data Management, Summary Statistics, </span>
<span class="fragment">Workflows, Development, Tool Integration, </span>
<span class="fragment"><font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, </span>
<span class="fragment">Image Processing, Visualization, </span>
<span class="fragment">Networking, System Administration, </span>
<span class="fragment">Partnerships, Funding, HR</span>
<span class="fragment"><font color="f27c30">...No big deal!</font></span>
</p>
</section>
<section>
<h2><font color="12a3d8">LORIS-CBRAIN INTEGRATION</font></h2>
<img src="images/Data_flow.jpg">
</section>
</section>
<section>
<section>
<table class="reveal">
<a href="Big_brain.html target="_blank"><h2>BigBrain</h2></a>
<tr>
<td width="56%" style="vertical-align: middle">
<a href="https://bigbrain.loris.ca/main.php" target="_blank"><img src="images/BigBrain.png"></a>
</td>
<td width="44%" style="vertical-align: middle">
<a href="http://science.sciencemag.org/content/340/6139/1472" target="_blank"><img src="images/BigBrain_paper.png"></a>
</td>
</tr></table>
</section>
<section data-background-video="images/Bigbrain_low.mp4" data-background-color="#000000">
<p class="fragment current-visible"><font size="9" color="blue">BigBrain - high resolution reference brain</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Multimodal integration into an anatomically realistic standard space</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Years of development</font></p>
<p class="fragment current-visible"><font size="9" color="blue">20 micron resolution</font></p>
<p class="fragment current-visible"><font size="9" color="blue">7404 histological slices</font></p>
<p class="fragment current-visible"><font size="9" color="blue">1 Terabyte dataset</font></p>
<p class="fragment current-visible"><font size="9" color="blue"><a href="https://bigbrain.humanbrainproject.org/#!{'layers':{' grey value: ':{'type':'image'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/8bit'_'transform':[[1_0_0_-70666600]_[0_1_0_-70000000]_[0_0_1_-58777700]_[0_0_0_1]]}_' tissue type: ':{'type':'segmentation'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/classif'_'selectedAlpha':0_'segments':['0'_'100']_'transform':[[1_0_0_-70666600]_[0_1_0_-72910000]_[0_0_1_-58777700]_[0_0_0_1]]}}_'navigation':{'pose':{'position':{'voxelSize':[21166.666015625_20000_21166.666015625]_'voxelCoordinates':[-3338.57958984375_856.3231811523438_-853.1627807617188]}}_'zoomFactor':1400706.647149517}_'perspectiveOrientation':[0.3140767216682434_-0.7418519854545593_0.4988985061645508_-0.3195493221282959]_'perspectiveZoom':1922235.5293810747}" target="_blank"><font color="f27c30"><small>Click to launch the Neuroglancer Viewer!</small></font></a></font></p>
</section>
</section>
<!-- BigBrain on LORIS -->
<section>
<section>
<h2>What is BigBrain?</h2>
<span class="fragment"><p>The <font color="12a3d8">BigBrain dataset</font> is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles <font color="f27c30">(Forschungszentrum Jülich)</font>, and Dr. Alan Evans <font color="12a3d8">(Montreal Neurological Institute)</font></p></span>
<p class="fragment"><font size="9" color="12a3d8">Available freely at <a href="https://bigbrain.loris.ca/main.php" target="_blank"><font color="f27c30">https://bigbrain.loris.ca</font></a></font></p>
</section>
<section data-background="images/bigbrain_data.png">
<h2><font color="222222">3D Volumes</font></h2>
</section>
<section data-background="images/3D_surface.png">
<h2><font color="222222">3D Surfaces</font></h2>
</section>
<section data-background="images/3D_classified.png">
<h2><font color="222222">3D Classified Volumes</font></h2>
</section>
<section>
<h2>Human Brain Mapping</h2>
<h5>How It's Made</h5>
<iframe width="640" height="360" data-src="https://bigbrain.loris.ca/images/media/BBvideo_HBM.mp4" frameboarder="0" gesture="media" allow="encrypted-media" allowfullscreen></iframe>
</section>
<section>
<h2>Visualization with Atelier 3D</h2>
<iframe width="640" height="360" data-src="https://www.youtube.com/embed/W2bmnhLV6R8" frameborder="0" gesture="media" allow="encrypted-media" allowfullscreen></iframe>
</section>
<section>
<h2>The Human Brain Project</h2>
<img width="50%" src="images/hbp_primary.png" align="center">
<a href="https://www.humanbrainproject.eu/en/explore-the-brain/" target="_blank"><p align="center"><small>Explore the Brain!</small></p></a>
</section>
<section>
<h2>HBP Neuroinformatics Platform</h2>
<img src="images/hbp_neuroinfo.png">
</section>
<section>
<h2>BigBrain Workshop 2017<br> Montreal</h2>
<a href="https://mcin-cnim.ca/bigbrain-workshop-2017-montreal-from-open-data-to-novel-applications/" target="_blank"<p>From open data to novel applications</p></a>
<img src="images/BigBrain_workshop2017.jpg">
</section>
</section>
<!--2015 release-->
<section data-transition="convex">
<section>
<h2>Latest Release 2015<br>Features</h2>
<span class="fragment"><p><font color="12a3d8">Improved aligment<br></span>
<span class="fragment">Optical balancing<br></span>
<span class="fragment">DeepZoom File Format<br></span>
<span class="fragment">3D Blocks<br></span>
<span class="fragment">3D ROI</span></font></p>
</section>
<section>
<h2>DeepZoom File Format</h2>
</section>
<section>
<h2>3D Blocks</h2>
</section>
<section>
<h2>3D ROI</h2>
</section>
</section>
<!-- Acknowledgements -->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/loris_team_2017.jpg" width="90%">
</td>
<td width="30%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> Alan Evans, Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!</font></small></p>
<p><font color="blue" size="4">LORIS team on left</font></p>
</td>
</tr></table>
</section>
</div>
</div>
<script src="lib/js/head.min.js"></script>
<script src="js/reveal.js"></script>
<script>
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