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feat: updated xray pages & lab profile page
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‎src/XRM.html‎

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@@ -57,22 +57,25 @@ <h2>Xray microscopy (XRM)</h2>
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<h4>Cellular- and micro- resolution of the rhizosphere</h4>
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<p>The success of the Xray instrument soon led to a smaller, but more powerful X-ray microscope to look at root-microbial interactions. Now the Topp lab can see the 3D subterranean world of roots nondestructively, at least for plants growing in large containers. The Topp lab’s X-ray CT and microscope facility for plant science at the Danforth Center is unique in the world.</p>
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<h4>Overview</h4>
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<p>To extend our imaging capabilities, we added a ZEISS Xradia 520 Versa X-ray microscope (XRM) in April 2018, supported by our research collaboration with Valent BioSciences, Sumitomo Chemical Company, and the Donald Danforth Plant Science Center. <br>
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This is currently the only lab-based XRM in the world dedicated exclusively to studying plant science, and our February 2022 publication in Plant Physiology (Duncan et al., 2022) describes how we have used XRM for a wide range of economically important plant species. <br>
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<a href="" class="image fit"><img src="images/XRM_Zeiss.png" alt="" /></a>
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<h4>How it works</h4>
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<p>Text...</p>
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<p>The XRM is a powerful and versatile instrument for generating detailed 3D volume data of delicate and complicated samples. The multiscale capability allows high magnification region-of-interest scans to be situated within the context of lower magnification scans of entire samples, without removing the sample from the instrument. The animations and screen shots below illustrate both the range of plant and soil samples that we have studied as well as the multiscale capability of the instrument. We’re also using XRM to study arbuscular mycorrhizal fungi (AMF) and their interaction with roots in situ. We developed various strategies for generating contrast of AMF structures for in vitro and in situ visualization of hyphae, spores, arbuscules, and vesicles.</p>
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<a href="" class="image fit"><img src="images/XRM_Zeiss_inside.png" alt="" /></a>
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<h4>Advantages and Specs of XRT </h4>
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<p>I’m thinking maybe we could use list or bullet points here for quick readability? <a href=""></a></p>
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<p></p>
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<a class="image fit"><img src="images/root-genetics.png" alt="" /></a>
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<h4>Project1</h4> Text describing image and project ... </div>
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<a class="image fit"><img src="images/xray-root.png" alt="" /></a>
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<h4>Project2</h4> Text describing image and project ... </div>
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<a class="image fit"><img src="images/xray-microscope-root.png" alt="" /></a>
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<h4>Project3</h4> Text describing image and project ... </div>
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<a class="image fit"><img src="images/modern-mesocosm.png" alt="" /></a>
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<h4>Project4</h4> Text describing image and project ... </div>
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<a class="image fit"><img src="videos/BrachyAMF_InSitu.m4v" alt="" /></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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<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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<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"><img src="videos/SoilAggregateOverlay.m4v" alt="" /></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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<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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<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"><img src="videos/SoybeanOverlay.m4v" alt="" /></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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<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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<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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‎src/XRT.html‎

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<h4>Xray CT for non-invasive 3D imaging of plant roots</h4>
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<p>A partnership with Valent BioSciences in 2016, along with funding from the National Science Foundation, brought one of these 8-ton machines to the Danforth Center.</p>
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<h4>Overview</h4>
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<p>X-ray tomography (XRT) is a valuable technology for non-destructive imaging both above and below the soil line, providing rich 3D image data of roots and the entire soil ecosphere. Our large industrial scale instrument is a North Star Imaging X5000, that combines a microfocus X-ray source and high resolution flat panel detector with a large interior cabinet and flexible motion control system, allowing high resolution non-destructive imaging over a wide range of sample sizes and densities. </p>
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<h4>How it works</h4>
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<p>The flat panel detector can be switched between portrait and landscape orientations according to sample shape and desired resolution. In addition, helical, tiling, and SubpiX scan modes significantly expand sample orientation and scan resolution options. The X5000 was installed in August 2016 and was made possible as part of a research collaboration with Valent BioSciences.</p>
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<h4>Advantages and Specs of XRT </h4>
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<h4>Project4</h4> Text describing image and project ... </div>
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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"><img src="videos/SegmentedMaizeRoots_XRT.mp4" alt="" /></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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<a class="image fit"><img src="videos/MaizeEar_XRT.m4v" alt="" /></a>
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<h4>Mature maize ear</h4> Text describing image and project ...
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<a class="image fit"><img src="videos/SorghumPanicle_XRT.m4v" alt="" /></a>
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<h4>Sorghum panicle</h4>
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<a class="image fit"><img src="videos/Grapes_XRT.mp4" alt="" /></a>
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<h4>Fresh bunch of grapes</h4>
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<a class="image fit"><img src="videos/Pepper_XRT.m4v" alt="" /></a>
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<h4>Fresh bell pepper</h4>
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<a class="image fit"><img src="videos/Pumpkin_XRT.m4v" alt="" /></a>
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<h4>Halloween pumpkin</h4> Text describing image and project ... </div>
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‎src/images/BrachyAMF_InSitu.m4v‎

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