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2024-07-15 14:30:46 +08:00
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<title>Bioxel Nodes - Bioxel Nodes Docs</title>
<title>Bioxel Nodes Handbook</title>
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<header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
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<a href="." title="Bioxel Nodes Handbook" class="md-header__button md-logo" aria-label="Bioxel Nodes Handbook" data-md-component="logo">
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<div class="md-header__ellipsis">
<div class="md-header__topic">
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Bioxel Nodes Docs
Bioxel Nodes Handbook
</span>
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<li class="md-tabs__item md-tabs__item--active">
<a href="." class="md-tabs__link">
Bioxel Nodes
</a>
</li>
<li class="md-tabs__item md-tabs__item--active">
<a href="." class="md-tabs__link">
<li class="md-tabs__item">
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BioxelNodes
Getting Started
</a>
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<a href="import/" class="md-tabs__link">
Visualizating any Bio-structure
</a>
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Reference
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<nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
<label class="md-nav__title" for="__drawer">
<a href="." title="Bioxel Nodes Docs" class="md-nav__button md-logo" aria-label="Bioxel Nodes Docs" data-md-component="logo">
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Bioxel Nodes Docs
Bioxel Nodes Handbook
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<li class="md-nav__item md-nav__item--active">
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
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BioxelNodes
Bioxel Nodes
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Bioxel Nodes
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Support 4D volumetric data
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Compatibile to Newer Version
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<h1 id="bioxel-nodes">Bioxel Nodes</h1>
<p><img alt="Static Badge" src="https://img.shields.io/badge/Blender-orange?style=for-the-badge&amp;logo=blender&amp;logoColor=white" />
<img alt="GitHub License" src="https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge" />
<img alt="GitHub Release" src="https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge" />
<img alt="GitHub Repo stars" src="https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge" /></p>
<p>Bioxel Nodes is a Blender add-on for scientific volumetric data visualization. It using Blender's powerful Geometry Nodes | Cycles to process and render volumetric data.</p>
<h2 id="about">About</h2>
<p>Before us, there have been many tutorials and add-ons for importing volumetric data into Blender. However, we found that there were many details that were not addressed in place, some scientific facts were ignored, and the volume rendering was not pretty enough. With Bioxel Nodes, you can easily import the volumetric data into Blender, and more importantly, it can quickly make a beautiful realistic rendering of it.</p>
<p>Below are some examples with Bioxel Nodes. Thanks to Cycles Render, the volumetric data can be rendered with great detail:</p>
<p>Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful <strong>Geometry Nodes</strong> and <strong>Cycles</strong> to process and render volumetric data.</p>
<p><img alt="cover" src="assets/cover.png" /></p>
<p>The "Bioxel" in "Bioxel Nodes", is a combination of the words "Bio-" and "Voxel". Bioxel is a voxel that stores biological data. We are developing a toolkit around Bioxel for better biological data visualization. but before its release, we made this Blender version of bioxels toolkit first, in order to let more people to have fun with volumetric data. <a href="https://omoolab.github.io/BioxelNodes/latest/getting-started">Getting Started</a></p>
<h2 id="supported-format">Supported Format</h2>
<ul>
<li>Fantastic rendering result, also support EEVEE NEXT</li>
<li>Support multiple formats</li>
<li>Support 4D volumetric data</li>
<li>All kinds of cutters</li>
<li>Simple and powerful nodes</li>
<li>Based on blender natively, can work without addon.</li>
</ul>
<p><strong>Click <a href="https://omoolab.github.io/BioxelNodes/latest/installation">Getting Started</a> to begin your journey into visualizing volumetric data!</strong></p>
<h2 id="support-multiple-formats">Support Multiple Formats</h2>
<table>
<thead>
<tr>
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<td>✅ pass</td>
</tr>
<tr>
<td>Meta</td>
<td>.mha, .mhd</td>
<td>yet</td>
</tr>
<tr>
<td>HDF5</td>
<td>.hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5</td>
<td>✅ pass</td>
</tr>
<tr>
<td>VTK</td>
<td>.vtk</td>
<td>yet</td>
</tr>
<tr>
<td>BioRad</td>
<td>.PIC, .pic</td>
<td>yet</td>
</tr>
<tr>
<td>Gipl</td>
<td>.gipl, .gipl.gz</td>
<td>yet</td>
</tr>
<tr>
<td>LSM</td>
<td>.lsm, .LSM</td>
<td>yet</td>
</tr>
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<td>MINC</td>
<td>.mnc, .MNC</td>
<td>yet</td>
</tr>
<tr>
<td>MRC</td>
<td>.mrc, .rec</td>
<td>yet</td>
</tr>
</tbody>
</table>
<h2 id="support-4d-volumetric-data">Support 4D volumetric data</h2>
<p><img alt="4d" src="assets/4d-time.gif" /></p>
<p>🥰 4D volumetric data can also be imported into Blender.</p>
<h2 id="support-eevee-next">Support EEVEE NEXT</h2>
<p><img alt="eevee" src="assets/eevee.gif" /></p>
<p>👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:</p>
<ol>
<li>Only one cutter supported.</li>
<li>EEVEE result is not that great as Cycles does.</li>
</ol>
<h2 id="known-limitations">Known Limitations</h2>
<ul>
<li>Sections cannot be generated (will be supported soon)</li>
<li>Time sequence volume not supported (will be supported soon)</li>
<li>Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE</li>
<li>Section surface cannot be generated when convert to mesh (will be supported soon)</li>
</ul>
<h2 id="compatibile-to-newer-version">Compatibile to Newer Version</h2>
<p><strong>Updating this addon may break old files, so read the following carefully before updating</strong></p>
<p>Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run <strong>Bioxel Nodes &gt; Save Staged Data</strong> to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.</p>
<p>After the addon update, your old project files may not work either, this may be because you had executed <strong>Save Staged Data</strong>. If so, you need to execute <strong>Bioxel Nodes &gt; Relink Nodes to Addon</strong> to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.</p>
<p>Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on <strong>Open Shading Language (OSL)</strong> in the Render Settings.</p>
<h2 id="roadmap">Roadmap</h2>
<ul>
<li>Better multi-format import experience</li>
<li>One-click bake model with texture</li>
<li>AI Segmentation to Generate Labels</li>
</ul>
<h2 id="to-upgrade-add-on">To Upgrade Add-on</h2>
<p>To upgrade from an older version of the add-on to the latest, you need to do the following:</p>
<ol>
<li>Remove the old version of Bioxel Nodes at Preferences &gt; Add-ons</li>
<li>Add the new version and restart Blender.</li>
</ol>
<p>It is not support editing the same blender file across add-on versions. In order to make sure that the previous file works properly. You need to save the staged data before upgrading ( read the last section of <a href="https://omoolab.github.io/BioxelNodes/latest/getting-started/#share-your-file">Getting Started</a> ).</p>
<p>But even then, there is still no guarantee that the new version of the add-on will work on the old blender file. Therefore, it is highly recommended to open a new blender file to start the creating, not based on the old one.</p>
<p>Alternatively, objects from the old file that have nothing to do with Bioxel Nodes could be append to the new blender file.</p>
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