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<!DOCTYPE html>
<html lang="en">
<head>
<title>FIIND Ferret Interactive Integrated Neurodevelopment Atlas</title>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
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<link rel="stylesheet" type="text/css" href="./css/main.css">
<link rel='shortcut icon' type='image/x-icon' href="./favicon.ico" />
<link href='https://fonts.googleapis.com/css?family=Montserrat' rel='stylesheet'>
<link href='https://fonts.googleapis.com/css?family=Raleway' rel='stylesheet'>
<link href="https://fonts.googleapis.com/css?family=Plaster" rel="stylesheet">
</head>
<body>
<!-- navigation bar -->
<!-- currently, the fixed top class is added, so it sticks to the top -->
<!-- data value of nav bar corresponds to id in each section -->
<nav class="navbar navbar-expand-lg fixed-top ">
<a class="navbar-brand" href="https://neuroanatomy.github.io/" target="_blank">
<div class="logo_naat"><p style="padding-left:2.7em;color:white;cursor:pointer;font-size:14px;font-weight:300;line-height:2.2;vertical-align: middle;">Neuroanatomie appliquée et théorique</p></div>
</a>
<button class="navbar-toggler landing-page myCollapsedMenuBarIcon" id="myMenuBtn" type="button" data-toggle="collapse" data-target="#myMenu" aria-controls="myMenu" aria-expanded="false" aria-label="Toggle navigation" style="padding:0;border:none; width:1.5em;height:1.5em;" onclick="this.blur();">
</button>
<div class="collapse navbar-collapse" id="myMenu" style="width:100%;">
<a class="navbar-brand" href="#myheader">
<div class="logo_fiind"></div>
</a>
<ul class="navbar-nav mr-4" >
<li class="nav-item">
<a class="nav-link" data-value="home" href="#">FIIND</a>
</li>
<li class="nav-item">
<a class="nav-link" id="datatablemri" href="./datatables/mri/" target="_blank">MRI</a>
</li>
<li class="nav-item">
<a class="nav-link" <a id="datatablehisto" href="./datatables/histology/" target="_blank">Histology</a>
</li>
<li class="nav-item">
<a class="nav-link" <a id="notebooks" href="./resources/" target="_blank">Notebooks</a>
</li>
<!--<li class="nav-item">
<a class="nav-link" data-value="projects" href="#">Projects</a>
</li>-->
</ul>
</div>
</nav>
<!-- my header -->
<header class="header" id="myheader">
<div class="overlay">
</div>
<div class="container">
<div class="description rectangle">
<div class="row">
<!-- left side logo -->
<div class="col-lg-4 col-md-4 col-xs-12">
<div class="fiindlogobig" style="max-width:100%;transform:translate(0,0)">
<img src="./images/logo/fiind_with-font-and-text_all.svg" class="img-fluid" alt="">
</div>
<br/>
</div>
<!-- right side text -->
<div class="col-lg-8 col-md-8 col-xs-12" style="position: relative;bottom:0em;vertical-align: bottom; vertical-align: text-bottom; padding-top:8em;padding-left:1em;">
<p style="vertical-align: bottom;position:absolute;bottom:0.3em;padding-right: 2em;">A project to create an online atlas of the development of the ferret brain, and to further the development of interactive tools to collaborate on the FIIND dataset.
</p>
</div>
</div>
</div>
</div>
</header>
<!-- FIIND project description -->
<div class="row mainpageparts" id="home">
<div class="container">
<h1>FIIND</h1>
<div class="row">
<!-- left side 1 -->
<div class="col-lg-4 col-md-4 col-sm-12">
<div data-aos="fade-in" data-aos-easing="linear" data-aos-duration="3000" data-aos-offset="0">
<img data-aos="fade-in" data-aos-easing="linear" data-aos-duration="3000" data-aos-offset="0" src="./images/landing_page/histo_1.jpg" style="width:100%;padding-top:2.8em;filter:grayscale(50%) contrast(100%) opacity(90%); -webkit-filter:grayscale(50%) contrast(100%) opacity(90%);"" class="img-fluid" alt="">
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<div>
<span>Histology of a 32 day old ferret</span>
</div>
<div><p><br></p></div>
</div>
<!-- right side 1 -->
<div class="col-lg-8 col-md-8 col-sm-12 desc">
<h3>Ferret interactive integrated neurodevelopment atlas</h3>
<p>Project FIIND is an international effort to create the most detailed description of the development of the ferret brain. The first days after birth in ferrets provide a unique view of the development of a complex brain. Unlike mice, ferrets develop a rich pattern of deep neocortical folds and cortico-cortical connections. Unlike humans and other primates, whose brains are well differentiated and folded at birth, ferrets are born with a very immature and completely smooth neocortex: folds, neocortical regionalisation and cortico-cortical connectivity develop in ferrets during the first days after birth. After a period of fast neocortical expansion, during which brain volume increases by up to a factor of 4 in 2 weeks, the ferret brain reaches its adult volume at about 6 weeks of age.
<br/><br/>
</p>
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<!-- left side 2 -->
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<div data-aos="fade-in" data-aos-easing="linear" data-aos-duration="3000" data-aos-offset="0">
<img src="./images/landing_page/ferrets.jpg" style="width:100%; filter:grayscale(50%) contrast(100%) opacity(90%); -webkit-filter:grayscale(60%) contrast(100%) opacity(90%);" class="img-fluid" alt="">
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<div>
<span>Ferrets as study model</span>
</div>
<div><p><br></p></div>
</div>
<!-- right side 2 -->
<div class="col-lg-8 col-md-8 col-sm-12 desc">
<h3>The ferret as an exceptional model for neuroimaging</h3>
<p>
Ferrets appear as an exceptional animal model to investigate the neurobiological correlates of the phenomena observed in human neuroimaging. Many of these phenomena, such as the relationship between brain folding, cortico-cortical connectivity and neocortical regionalisation cannot be investigated in mice, but can be investigated in ferrets.<br>
<br>
</p>
</div>
<!-- left side 3 -->
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<div data-aos="fade-in" data-aos-duration="3000" data-aos-offset="0">
<img src="./images/landing_page/collaboration.jpg" style="width:100%;filter:grayscale(50%) contrast(100%) opacity(90%); -webkit-filter:grayscale(50%) contrast(100%) opacity(90%);" class="img-fluid" alt="">
</div>
<div>
<span>An open database with integrated tools for collaborative annotation</span>
</div>
<div><p><br></p></div>
</div>
<!-- right side 3 -->
<div class="col-lg-8 col-md-8 col-sm-12 desc">
<h3>An open science project</h3>
<p>We are constituting an open, collaborative atlas of ferret brain development, integrating multi-modal and multi-scale data. We acquired data from many animals, from newborns to adults, using high-resolution MRI, diffusion weighted imaging (DWI) and high-throughput histology. Brains were sectioned at 30 μm and scanned at 0.25 μm of resolution, and processed for real-time multi-scale visualisation. We have built a web-platform to integrate an interactive multi-scale visualisation of the data. Using our combined expertise in computational neuroanatomy, multi-modal neuroimaging, neuroinformatics, and the development of inter-species atlases, we have built an open-source web platform to allow the collaborative, online, creation of atlases of the development of the ferret brain. The web platform allows researchers to access and visualise interactively the MRI and histology data. It also allows researchers to create collaborative, human curated, 3D segmentations of brain structures, as well as vectorial atlases. Our work should provide a first integrated atlas of ferret brain development, and the basis for an open platform for the creation of collaborative multi-modal, multi-scale, multi-species atlases.
</p>
</div>
</div>
</div>
</div>
<!-- Data -->
<div class="row mainpageparts" id="data">
<div class="container">
<h1>Data</h1>
<!-- visual head image of section -->
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<!--<video class="visualintro" autoplay muted style="object-fit:cover;width:100%;height:300px;">
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<div>
<a id="datatablemri" href="./datatables/mri/" target="_blank">
<span>Magnetic Resonance Imaging: T2w & DWI data</span>
</a>
</div>
<div><p><br></p></div>
</div>
<!-- right side 1 -->
<div class="col-lg-8 col-md-8 col-sm-12 desc">
<h3>Magnetic Resonance Imaging data</h3>
<p>
<b style="font-weight:900;">T2 weighted & Diffusion weighted imaging data</b><br/>
We have acquired data for 28 ferrets (4 animals per time point from P0 to adults), using high-resolution MRI and diffusion weighted imaging (DWI). The T2 weighted images have a 120µm isotropic resolution, and the DWI data has been acquired at 240µm istropic resolution.
<br/>We have developed an open-source pipeline to segment and produce – online – 3D reconstructions of brain MRI data. We provide a <a href="./datatables/mri/" target="_blank" style="color:white; cursor: pointer">web framework</a> for the interactive visualisation of the data, and a real-time collaborative annotation.
<br/>More details can be found in the <a href="https://riojournal.com/article/25312/" target="_blank" style="color:white; cursor: pointer">initial grant proposal.</a><br/>
<br/>
</p>
</div>
<!-- left side 2 -->
<div class="col-lg-4 col-md-4 col-sm-12">
<div data-aos="fade-in" data-aos-duration="3000" data-aos-offset="0">
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</div>
<div>
<a id="datatablehisto" href="./datatables/histology/" target="_blank">
<span>Histological data: Nissl & NeuN staining</span>
</a>
</div>
<div><p><br></p></div>
</div>
<!-- right side 2 -->
<div class="col-lg-8 col-md-8 col-sm-12 desc">
<h3>High resolution histological data</h3>
<p>
Whole brains (cerebrum and cerebellum) of 20 specimens (4 brains at each time point from P0 to P32) have been processed using high-throughput 3D histology, staining for cytoarchitectonic landmarks (Nissl and NeuN). Brains were sectioned at 30 μm (P32, P16, P8) and 40 µm (P4, P0), stained, scanned at 0.25 μm of resolution, and processed for real-time multi-scale visualisation.
<br/>We built a <a href="./datatables/histology/" target="_blank" style="color:white; cursor: pointer">web-platform</a> to integrate an interactive multi-scale visualisation of the data, and provide a real-time annotation framework for the creation of collaborative multi-modal, multi-scale, multi-species atlases.
<br/>
The availability of both modalities at the same ages allows to relate the MRI data with multi-dimensional cell-scale information during development.
<br/>
More details can be found in the <a href="https://riojournal.com/article/25312/" target="_blank" style="color:white; cursor: pointer">initial grant proposal.</a><br/><br/>
<br/>
</p>
</div>
</div>
</div>
</div>
<!-- Data Overview: Gallery with filters -->
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<h1>Overview of the datasets</h1>
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<a class="btn btn-outline-secondary filter" data-rel="all">All</a>
<a class="btn btn-outline-secondary filter" data-rel="structMRI">T2w</a>
<a class="btn btn-outline-secondary filter" data-rel="DWI">DWI</a>
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<a class="btn btn-outline-secondary filter" data-rel="neun">NeuN</a>
<a class="btn btn-outline-secondary filter" data-rel="P0">P0</a>
<a class="btn btn-outline-secondary filter" data-rel="P2">P2</a>
<a class="btn btn-outline-secondary filter" data-rel="P4">P4</a>
<a class="btn btn-outline-secondary filter" data-rel="P8">P8</a>
<a class="btn btn-outline-secondary filter" data-rel="P16">P16</a>
<a class="btn btn-outline-secondary filter" data-rel="P32">P32</a>
<a class="btn btn-outline-secondary filter" data-rel="adult">Adult</a>
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<h1>Partners</h1>
<!-- Institut Pasteur -->
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<a href="https://neuroanatomy.github.io/"
target="_blank"
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<img src="./images/logo/pasteur.svg" class="partner-logos" alt="">
<div style="display:table-cell">
<a href="https://neuroanatomy.github.io/"
target="_blank"
style="color:white; cursor: pointer;">
Groupe de neuroanatomie appliquée et théorique, Institut Pasteur, France (Roberto Toro)
</a>
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</a>
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</div>
</div>
</div>
<!-- Radboud U -->
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<a href="https://www.ru.nl/donders/research/theme-4-neural-computation-neurotechnology/research-groups-theme-4/neuroinformatics/"
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<img src="./images/logo/radboud.svg" class="partner-logos" alt="">
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<a href="https://www.ru.nl/donders/research/theme-4-neural-computation-neurotechnology/research-groups-theme-4/neuroinformatics/"
target="_blank"
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Neuroinformatics research group, Radboud University Nijmegen, The Netherlands (Paul Tiesinga)
</a>
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</a>
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</div>
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<!-- MIRCen -->
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<img src="./images/logo/cea.svg" class="partner-logos" alt="">
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MIRCen, Commisariat aux Énergies Alternatives, France (Thierry Delzescaux)
</a>
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</a>
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</div>
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<!-- MCGill -->
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McGill Centre for Integrative Neuroscience, Quebec, Canada (Alan Evans)
</a>
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</a>
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</div>
</div>
</div>
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Rembrandt Bakker (Radboud University Nijmegen, The Netherlands)
</a>
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<!-- Victor -->
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Víctor Borrell Franco (Instituto de Neurociencias de Alicante, Spain)
</a>
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<!-- Isabel Reillo -->
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Isabel Reillo (Instituto de Neurociencias de Alicante, Spain)
</a>
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Camino de Juan Romero (Instituto de Neurociencias de Alicante, Spain)
</a>
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</div>
</div>
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<!-- NSA -->
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<div class="col-lg-12 col-md-12 col-sm-12">
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<a href="https://www.neuroscienceassociates.com/"
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Robert C. Switzer (Neuroscience Associates, USA)
</a>
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</div>
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<a href="http://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/NeuroSpin.aspx/"
target="_blank"
style="color:white; cursor: pointer;line-height:3;">
Jean-François Mangin (NeuroSpin, France)
</a>
</div>
</div>
</div>
</div>
<!-- Sébastien Mériaux -->
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<a href="http://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/NeuroSpin.aspx/"
target="_blank"
style="color:white; cursor: pointer;line-height:3;">
Sébastien Mériaux (NeuroSpin, France)
</a>
</div>
</div>
</div>
</div>
<!-- Benoit Larrat -->
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<a href="http://joliot.cea.fr/drf/joliot/Pages/Entites_de_recherche/NeuroSpin.aspx/"
target="_blank"
style="color:white; cursor: pointer;line-height:3;">
Benoit Larrat (NeuroSpin, France)
</a>
</div>
</div>
</div>
</div>
</div>
</div>
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<h1>Funding</h1>
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<img class="funder" src="./images/logo/hbp.png" title="Human Brain Project" class="img-fluid" alt="">
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