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[feat] vimeo hosted videos
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src/LICENSE.txt renamed to LICENSE.txt

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src/README.txt renamed to README.txt

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src/XRM.html renamed to XRM.html

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<div id="logo">
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<h1><a href="index.html">Topp Roots Lab</a></h1> <span> </span> </div>
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<!-- Nav -->
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<!-- Nav -->
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<nav id="nav">
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<ul>
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<li><a href="index.html">Welcome</a></li>
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<li class = current><a href="research.html">Research</a>
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<ul>
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<li><a href="XRT.html">Xray CT</a></li>
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<li><a href="XRM.html">Xray Microscopy</a></li>
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</ul></li>
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<li><a href="publications.html">Publications</a></li>
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<li><a href="index.html">Home</a></li>
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<li><a href="news.html">News</a>
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<li class="current"><a href="research.html">Research</a>
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<ul>
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<li><a href="research.html">Research overview</a></li>
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<li><a href="XRT.html">Xray CT</a></li>
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<li><a href="XRM.html">Xray Microscopy</a></li>
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</ul>
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</li>
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<li><a href="publications.html">Papers</a></li>
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<li> <a href="tools.html">Tools</a>
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<ul>
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<li><a href="https://github.com/Topp-Roots-Lab/TopoRoot">TopoRoot</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">3-D Root Crown Analysis Pipeline</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/Gia3D">Gia3D</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">Root timeseries analysis</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">3-D Root
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Crown Analysis Pipeline</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/Gia3D">GiaRoots</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">Root timeseries
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analysis</a></li>
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</ul>
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</li>
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<li><a href="lab.html">Lab</a></li>
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<li> <a href="Data.html">Data</a></li>
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<li><a href="lab.html">Team</a></li>
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<li><a href="join.html">Join</a></li>
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</ul>
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</nav>
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<div class="grid">
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<a class="image fit"><img src="videos/BrachyAMF_InSitu.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:72% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779391743?h=985cf72fdf&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="BrachyAMF_InSitu"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Root-microbe colonization</h4> Roots of Brachypodium colonized by Rhizophagus irregularis, contrasted with osmium and imaged by XRM in situ.
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<a class="image fit"><img src="videos/CarrotRootAMF_OsO4.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:60.61% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396289?h=e709b47919&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="CarrotRootAMF_OsO4.m4v"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Carrot root AMF</h4> In vitro carrot root cultures colonized by R. irregularis, contrasted with osmium tetroxide.
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<a class="image fit"><img src="videos/CarrotRootAMF_WGA_Au.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:71.57% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396320?h=8fb4fe808b&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="CarrotRootAMF_WGA_Au"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Carrot root AMF</h4> In vitro carrot root cultures colonized by R. irregularis, contrasted with Wheat Germ Agglutinin conjugated to 40nm gold particles.
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<a class="image fit"><div style="padding:59.9% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396371?h=0bd98d7363&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="SoilAggregateOverlay"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Soil aggregate</h4> Multiscale overlaid scans of soil aggregate, part of a project to use X-ray imaging to evaluate pore space from soils under differing management strategies.
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<a class="image fit"><img src="videos/PennycressOverlay.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396353?h=468bb7f0c2&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="PennycressOverlay"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Pennycress pod</h4> Low magnification scan of a pennycress pod with overlaid high magnification scan of two developing seeds, with individual cell layers and developing cotyledons visible.
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<a class="image fit"><img src="videos/ArabidopsisFlowerOverlay.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:64.92% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779391728?h=03cfa89442&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="ArabidopsisFlowerOverlay.m4v"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Arabidopsis flower</h4> Multiscale overlaid scans of Arabidopsis flower with long slender ovary containing multiple ovules, surrounded by pollen-filled anthers.
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<a class="image fit"><div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396396?h=79ef2dab80&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="SoybeanOverlay"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Soil aggregate</h4> Multiscale overlaid scans of soybean flower with ovary containing three ovules, surrounded by pollen-containing anthers. Polar nuclei and synergids are visible in the high magnification scan of a single ovule.
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<a class="image fit"><img src="videos/SoyOvule20X_FlyThru.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:64.96% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396475?h=a4508c1fba&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="SoyOvule20X_FlyThru"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Soybean ovule</h4> Fly-through animation of 2D digital slices through a developing soybean ovule, showing rich cell-level detail.
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<a class="image fit"><img src="videos/SoyNoduleOverlay.m4v" alt="" /></a>
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<a class="image fit"><div style="padding:80.72% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779396452?h=88a32c4235&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="SoyNoduleOverlay"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Soybean nodule</h4> Multiscale overlaid scans of soybean nodule formed by the nitrogen-fixing bacterium Bradyrhizobium japonicum. Host vascular bundles are evident surrounding the nodule, and the hundreds of bacteroids with bright nuclei are visible.
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<a data-flickr-embed="true" data-header="true" data-footer="true" href="https://www.flickr.com/photos/197041608@N05/albums/72177720304136404" title="XRM"><img src="https://live.staticflickr.com/65535/52536011182_13b39f3ebc_b.jpg" width="1024" height="768" alt="XRM"></a><script async src="//embedr.flickr.com/assets/client-code.js" charset="utf-8"></script>
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<a data-flickr-embed="true" data-header="true" data-footer="true" href="https://www.flickr.com/photos/197041608@N05/52536011182/in/photostream/" title="CarrotRootAMF_OsO4_1"><img src="https://live.staticflickr.com/65535/52536011182_13b39f3ebc_b.jpg" width="1024" height="660" alt="CarrotRootAMF_OsO4_1"></a><script async src="//embedr.flickr.com/assets/client-code.js" charset="utf-8"></script>
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<a data-flickr-embed="true" data-header="true" data-footer="true" data-context="true" href="https://www.flickr.com/photos/197041608@N05/52536011182/in/album-72177720304136404/" title="CarrotRootAMF_OsO4_1"><img src="https://live.staticflickr.com/65535/52536011182_13b39f3ebc_b.jpg" width="1024" height="660" alt="CarrotRootAMF_OsO4_1"></a><script async src="//embedr.flickr.com/assets/client-code.js" charset="utf-8"></script>
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<!-- add the following after the youtube embed/url "&autoplay=1&?rel=0" -->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/zVu_c1kOn9U?controls=0&autoplay=1&?rel=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
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src/XRT.html renamed to XRT.html

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<div id="logo">
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<h1><a href="index.html">Topp Roots Lab</a></h1> <span> </span> </div>
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<!-- Nav -->
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<ul>
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<li><a href="index.html">Welcome</a></li>
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<li class = current><a href="research.html">Research</a>
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<ul>
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<li><a href="XRT.html">Xray CT</a></li>
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<li><a href="XRM.html">Xray Microscopy</a></li>
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</ul></li>
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<li><a href="publications.html">Publications</a></li>
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<li><a href="index.html">Home</a></li>
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<li><a href="news.html">News</a>
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<li class="current"><a href="research.html">Research</a>
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<ul>
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<li><a href="research.html">Research overview</a></li>
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<li><a href="XRT.html">Xray CT</a></li>
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<li><a href="XRM.html">Xray Microscopy</a></li>
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</ul>
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</li>
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<li><a href="publications.html">Papers</a></li>
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<li> <a href="tools.html">Tools</a>
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<ul>
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<li><a href="https://github.com/Topp-Roots-Lab/TopoRoot">TopoRoot</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">3-D Root Crown Analysis Pipeline</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/Gia3D">Gia3D</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">Root timeseries analysis</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline">3-D Root
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Crown Analysis Pipeline</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/Gia3D">GiaRoots</a></li>
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<li><a href="https://github.com/Topp-Roots-Lab/timeseries_analysis">Root timeseries
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analysis</a></li>
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<a class="image fit"><img src="videos/MaizeRootCrown_XRT.m4v" alt="" /></a>
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<h4>Excavated maize root crown</h4> Text describing image and project ...
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<a class="image fit"><div style="padding:67.11% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779397539?h=868093d2ac&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="MaizeRootCrown_XRT"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Excavated maize root crown</h4>
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<a class="image fit"><div style="padding:55.83% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779397614?h=85ae310b5e&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="SegmentedMaizeRoots_XRT"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>In-situ maize root</h4> Maize root system that has been computationally segmented from a high resolution scan of roots growing in soil
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<h4>Mature maize ear</h4>
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<h4>Fresh bunch of grapes</h4>
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<a class="image fit"><div style="padding:66.63% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/779397571?h=8b59319139&loop=1&autoplay=1&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="Pepper_XRT"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script></a>
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<h4>Halloween pumpkin</h4> Text describing image and project ... </div>
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<h4>Halloween pumpkin</h4></div>
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<li><a href="tools.html">Tools & resources</a></li>
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<li><a href="lab.html">Lab members</a></li>
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<li><a href="lab.html">Lab team</a></li>
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<li><a href="https://www.google.com/maps/dir/?api=1&destination=38.674333,-90.3971893">Find us</a></li>
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<li><a href="join.html">Join us</a></li>
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</ul>

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