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<a href="#dependency-installation" class="md-nav__link">
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Dependency Installation
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Prepare Your Data
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Basic Usage
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Import Volume Data
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Share Your File
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Features
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Features & Options
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<a href="#dependency-installation" class="md-nav__link">
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<a href="#prepare-your-data" class="md-nav__link">
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Dependency Installation
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Prepare Your Data
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<a href="#import-volume-data" class="md-nav__link">
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<span class="md-ellipsis">
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Basic Usage
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Import Volume Data
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</span>
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</a>
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Share Your File
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@@ -599,38 +617,76 @@
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<h1 id="getting-started">Getting Started</h1>
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<p>Currently only support Blender 4.0 or above, make sure you have the correct version of Blender.</p>
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<h3 id="add-on-installation">Add-on Installation</h3>
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<h2 id="add-on-installation">Add-on Installation</h2>
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<p>Download the latest version https://github.com/OmooLab/BioxelNodes/releases/latest<br />
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In Blender, <code>Edit - Preferences - Add-ons - Install</code>, select the <code>BioxelNodes_{version}.zip</code> you just downloaded.</p>
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<h3 id="dependency-installation">Dependency Installation</h3>
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<p>The add-on requires a third-party python dependency called SimpleITK, click the Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After the Installation, <strong>restart blender once</strong>.</p>
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In Blender, Edit > Preferences > Add-ons > Install, select the <code>BioxelNodes_{version}.zip</code> you just downloaded.</p>
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<p>The add-on requires a third-party python dependency called SimpleITK, click <code>Install SimpleITK</code> button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After that, click <code>Reboot Blender</code> button.</p>
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<p><img alt="dependency" src="../assets/dependency.png" /></p>
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<p>This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror.</p>
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<h3 id="basic-usage">Basic Usage</h3>
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<p>First you need to have your volumetric data ready. If not, you can access open research data from <a href="https://datadryad.org">Dryad</a> (Dryad publishes data exclusively under a <a href="https://creativecommons.org/public-domain/cc0/">Creative Commons Public Domain License</a>)</p>
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<p>Note: Make sure one folder contains only one sequence, multiple sequences need to be manually split into different folders first.</p>
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<p>In Blender, <code>File - Import - Volume Data as Bioxels</code>, select <strong>one</strong> of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import, but this is limited to .dcm format files)</p>
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<h2 id="prepare-your-data">Prepare Your Data</h2>
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<p>First you need to have your volumetric data ready. If not, you can access open research data from list below：</p>
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<table>
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<thead>
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<tr>
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<th>Source</th>
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<th>Object</th>
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<tbody>
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<tr>
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<td><a href="https://datadryad.org">Dryad</a></td>
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<td>Open Research Data</td>
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</tr>
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<tr>
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<td><a href="https://openorganelle.janelia.org/datasets">OpenOrganelle</a></td>
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<td>Cells</td>
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</tr>
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<tr>
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<td><a href="https://www.embodi3d.com/files/category/37-medical-scans/">Embodi3D</a></td>
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<td>Medical Images</td>
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</tr>
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<tr>
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<td><a href="https://github.com/sfikas/medical-imaging-datasets">Github</a></td>
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<td>Medical Images</td>
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</tr>
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<tr>
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<td><a href="https://nhsx.github.io/open-source-imaging-data-sets/">NIHR</a></td>
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<td>Medical Images</td>
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</tr>
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<tr>
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<td><a href="http://medicaldecathlon.com/">Medical Segmentation Decathlon</a></td>
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<td>Medical Images</td>
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</tr>
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<tr>
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<td><a href="https://www.allencell.org/3d-cell-viewer.html">Allen Cell Explorer</a></td>
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<td>Cells</td>
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</tr>
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<tr>
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<td><a href="https://www.nlm.nih.gov/research/visible/visible_human.html">Visible Human Project</a></td>
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<td>Medical Images</td>
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</tr>
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</tbody>
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</table>
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<h2 id="import-volume-data">Import Volume Data</h2>
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<p>File > Import > Volume Data as Bioxels, select <strong>one</strong> of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import)</p>
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<p><img alt="importing" src="../assets/importing.png" /></p>
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<p>It may take a while to read data. After finishing reading, it will pop up a dialog box</p>
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<p><img alt="import dialog" src="../assets/import_dialog.png" /></p>
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<p><img alt="import dialog" src="../assets/import-dialog.png" /></p>
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<p>Ignore the options, just click OK!</p>
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<p>After importing, the necessary nodes are automatically added, the reconstruction and shader are created, and then turned on the cycles rendering to directly see the result.</p>
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<p>After importing, the necessary nodes are automatically added, the reconstruction and shader are created. Click select Bioxels Object, and open the Geometry Nodes panel, change the "Threshold" in segment node.</p>
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<p><img alt="segment node" src="../assets/segment-node.png" /></p>
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<p>and then turned on the cycles rendering to directly see the result.</p>
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<p><img alt="result" src="../assets/result.png" /></p>
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<p>Click select Bioxels Object, and open the Geometry Nodes panel to see the following node graph:</p>
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<p><img alt="segment node" src="../assets/segment_node.png" /></p>
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<p>You can change the "Threshold" to modify the reconstruction model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values.</p>
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<p>The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure:</p>
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<p><img alt="general graph" src="../assets/general_graph.png" /></p>
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<p>Currently there are 3 types of nodes</p>
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<ul>
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<li>Segmentation nodes, responsible for splitting the volume into a reconstructed model (we call them "Segment").</li>
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<li>Shader nodes, responsible for giving shader to the Segment.</li>
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<li>Slicer nodes, responsible for partially cutting the Segment.</li>
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</ul>
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<p>For example:</p>
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<p><img alt="general graph example" src="../assets/general_graph_example.png" /></p>
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<p>You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object.</p>
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<p><img alt="bake node" src="../assets/bake_node.png" /></p>
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<h2 id="share-your-file">Share Your File</h2>
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<p>The VDB cache and the Bioxel nodes are not reachable to computers if you don't save them. If you need to give your blender file to someone else, you will need to perform the following steps:</p>
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<ol>
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<li>Save your blender file</li>
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<li>Click Scene > Bioxels > Save All Bioxels in the Properties panel.</li>
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<li>Click Scene > Custom Nodes > Save All Custom Nodes under the Properties panel.</li>
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</ol>
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<p><img alt="before sharin" src="../assets/before-sharing.png" /></p>
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<p>After that, both the VDB cache and the Bioxel nodes are stored in relative locations. When you share a file with someone, pack the entire directory so that the resources are not lost. The other person will be able to load correctly, regardless of whether they have BioxelNodes installed.</p>
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@@ -677,13 +733,13 @@ In Blender, <code>Edit - Preferences - Add-ons - Install</code>, select the <cod
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<a href="../features/" class="md-footer__link md-footer__link--next" aria-label="Next: Features">
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<a href="../features/" class="md-footer__link md-footer__link--next" aria-label="Next: Features & Options">
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<div class="md-footer__title">
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Next
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<div class="md-ellipsis">
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Features
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Features & Options
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</div>
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</div>
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<div class="md-footer__button md-icon">
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