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<!DOCTYPE HTML>
<!--
Verti by HTML5 UP
html5up.net | @ajlkn
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
-->
<html lang="en">
<head>
<title>Topp Lab</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<link rel="stylesheet" href="assets/css/main.css" /> </head>
<body class="is-preload no-sidebar">
<div id="page-wrapper">
<!-- Header -->
<div id="header-wrapper">
<header id="header" class="container">
<!-- Logo -->
<div id="logo">
<h1><a href="index.html">Topp Roots Lab</a></h1> <span> </span> </div>
<!-- Nav -->
<nav id="nav">
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="news.html">News</a>
<li><a href="research.html">Research</a>
<ul>
<li><a href="research.html">Research overview</a></li>
<li><a href="XRT.html">Xray CT</a></li>
<li><a href="XRM.html">Xray Microscopy</a></li>
</ul>
</li>
<li><a href="publications.html">Papers</a></li>
<li class="current"> <a href="tools.html">Tools</a>
<ul>
<li><a href="https://github.com/Topp-Roots-Lab/TopoRoot">TopoRoot</a></li>
<li><a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">3-D Root
Crown Analysis Pipeline</a></li>
<li><a href="https://github.com/Topp-Roots-Lab/Gia3D">GiaRoots</a></li>
<li><a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">Root timeseries
analysis</a></li>
</ul>
</li>
<li> <a href="data.html">Data</a></li>
<li><a href="lab.html">Team</a></li>
<li><a href="join.html">Join</a></li>
</ul>
</nav>
</header>
</div>
<!-- Main -->
<div id="main-wrapper">
<div class="container">
<div class="row gtr-200">
<div class="col-12 col-12-medium">
<!-- Sidebar -->
<div id="sidebar">
<section class="widget thumbnails">
<h2>Tools & resources</h2>
<div class="grid">
<div class="row gtr-50">
<div class="col-3">
<h4>TopoRoot</h4>
<p>Method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images <a href="https://github.com/Topp-Roots-Lab/TopoRoot">[github]</a></p>
</div>
<div class="col-9">
<a href="https://github.com/Topp-Roots-Lab/TopoRoot" class="image fit"><img src="images/toporoot-pipeline.png" alt="" /></a>
</div>
<div class="col-3">
<h4>3-D Root Crown Analysis Pipeline</h4>
<p>Pipeline for segmentation of root crowns excavated from field and imaged using Xray CT <a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">[github]</a></p>
</div>
<div class="col-9">
<a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline" class="image fit"><img src="images/3d-root-crown-analysis-pipeline.png" alt="" /></a>
</div>
<div class="col-3">
<h4>Gia3D</h4>
<p>Root3D skeleton trait extraction <a href="https://github.com/Topp-Roots-Lab/Gia3D">[github]</a></p>
</div>
<div class="col-9">
<a href="https://github.com/Topp-Roots-Lab/Gia3D" class="image fit"><img src="images/Gia3D.png" alt="" /></a>
</div>
<div class="col-3">
<h4>Root timeseries analysis</h4>
<p>R scripts to analyze and visualize root traits over time from DynamicRoots-generated files <a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">[github]</a></p>
</div>
<div class="col-9">
<a href="https://github.com/Topp-Roots-Lab/timeseries_analysis" class="image fit"><img src="images/timeseries_analysis.png" alt="" /></a>
</div>
</div>
</div>
</section>
</div>
</div>
</div>
</div>
</div>
<!-- Footer -->
<div id="footer-wrapper">
<footer id="footer" class="container">
<div class="row">
<div class="col-9 col-6-medium col-12-small">
<!-- Links -->
<section class="widget links">
<h3>Site map</h3>
<ul class="style2">
<li><a href="index.html">Home</a></li>
<li><a href="research.html">Research</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="tools.html">Tools & resources</a></li>
<li><a href="lab.html">Lab members</a></li>
<li><a href="https://www.google.com/maps/dir/?api=1&destination=38.674333,-90.3971893">Find us</a></li>
<li><a href="join.html">Join us</a></li>
</ul>
</section>
</div>
<div class="col-3 col-6-medium col-12-small">
<!-- Contact -->
<section class="widget contact last">
<h3>Contact</h3>
<ul>
<li><a href="https://twitter.com/RootDevo" class=" icon brands fa-twitter"><span class="label">Twitter</span></a></li>
<li><a href="mailto:CTopp@danforthcenter.org" class="icon brands fa-telegram"><span class="label">Email</span></a></li>
<li><a href="https://www.google.com/maps/dir/?api=1&destination=38.674333,-90.3971893" class="icon brands fa-safari"><span class="label">Address</span></a></li>
<li><a href="https://scholar.google.com/citations?user=-L6lz1IAAAAJ" class="icon brands fa-google"><span class="label">Google scholar</span></a></li>
<li><a href="https://github.com/Topp-Roots-Lab/Topp-Roots-Lab.github.io" class="icon brands fa-github"><span class="label">Github</span></a></li>
</ul>
</section>
</div>
</div>
<div class="row">
<div class="col-12">
<div id="copyright">
<ul class="menu">
<li>© Christopher Topp [All rights reserved]</li>
<li>designed using Bootstrap 4.0</li>
<li>hosted on <i class="fab fa-github"></i></li>
<li>Source code available <a href="https://github.com/Topp-Roots-Lab/Topp-Roots-Lab.github.io">here</a></li>
<li>and maintained by the lab</li>
<li>Design: <a href="https://html5up.net">HTML5 UP</a></li>
</ul>
</div>
</div>
</div>
</footer>
</div>
</div>
<!-- Scripts -->
<script src="assets/js/jquery.min.js"></script>
<script src="assets/js/jquery.dropotron.min.js"></script>
<script src="assets/js/browser.min.js"></script>
<script src="assets/js/breakpoints.min.js"></script>
<script src="assets/js/util.js"></script>
<script src="assets/js/main.js"></script>
</body>
</html>