Files
Bioxel/0.2.x/index.html

733 lines
23 KiB
HTML
Executable File

<!doctype html>
<html lang="en" class="no-js">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="description" content="Bioxel Nodes is a Blender add-on for scientific volumetric data visualization.">
<meta name="author" content="OmooLab">
<link rel="canonical" href="https://omoolab.github.io/BioxelNodes/0.2.x/">
<link rel="next" href="getting-started/">
<link rel="icon" href="assets/images/favicon.png">
<meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.22">
<title>Bioxel Nodes - Bioxel Nodes Docs</title>
<link rel="stylesheet" href="assets/stylesheets/main.732c4fb1.min.css">
<link rel="stylesheet" href="assets/stylesheets/palette.06af60db.min.css">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Open+Sans:300,300i,400,400i,700,700i%7CCascadia+Code:400,400i,700,700i&display=fallback">
<style>:root{--md-text-font:"Open Sans";--md-code-font:"Cascadia Code"}</style>
<link rel="stylesheet" href="assets/_mkdocstrings.css">
<link rel="stylesheet" href="stylesheets/extra.css">
<script>__md_scope=new URL(".",location),__md_hash=e=>[...e].reduce((e,_)=>(e<<5)-e+_.charCodeAt(0),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
</head>
<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="black" data-md-color-accent="indigo">
<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
<label class="md-overlay" for="__drawer"></label>
<div data-md-component="skip">
<a href="#bioxel-nodes" class="md-skip">
Skip to content
</a>
</div>
<div data-md-component="announce">
</div>
<div data-md-color-scheme="default" data-md-component="outdated" hidden>
</div>
<header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
<nav class="md-header__inner md-grid" aria-label="Header">
<a href="." title="Bioxel Nodes Docs" class="md-header__button md-logo" aria-label="Bioxel Nodes Docs" data-md-component="logo">
<img src="assets/logo.png" alt="logo">
</a>
<label class="md-header__button md-icon" for="__drawer">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2Z"/></svg>
</label>
<div class="md-header__title" data-md-component="header-title">
<div class="md-header__ellipsis">
<div class="md-header__topic">
<span class="md-ellipsis">
Bioxel Nodes Docs
</span>
</div>
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">
Bioxel Nodes
</span>
</div>
</div>
</div>
<form class="md-header__option" data-md-component="palette">
<input class="md-option" data-md-color-media="(prefers-color-scheme)" data-md-color-scheme="default" data-md-color-primary="black" data-md-color-accent="indigo" aria-label="Switch to light mode" type="radio" name="__palette" id="__palette_0">
<label class="md-header__button md-icon" title="Switch to light mode" for="__palette_1" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><!--! Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2024 Fonticons, Inc.--><path d="M448 256c0-106-86-192-192-192v384c106 0 192-86 192-192zM0 256a256 256 0 1 1 512 0 256 256 0 1 1-512 0z"/></svg>
</label>
<input class="md-option" data-md-color-media="(prefers-color-scheme: light)" data-md-color-scheme="default" data-md-color-primary="black" data-md-color-accent="indigo" aria-label="Switch to dark mode" type="radio" name="__palette" id="__palette_1">
<label class="md-header__button md-icon" title="Switch to dark mode" for="__palette_2" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2024 Fonticons, Inc.--><path d="M144.7 98.7c-21 34.1-33.1 74.3-33.1 117.3 0 98 62.8 181.4 150.4 211.7-12.4 2.8-25.3 4.3-38.6 4.3C126.6 432 48 353.3 48 256c0-68.9 39.4-128.4 96.8-157.3zm62.1-66C91.1 41.2 0 137.9 0 256c0 123.7 100 224 223.5 224 47.8 0 92-15 128.4-40.6 1.9-1.3 3.7-2.7 5.5-4 4.8-3.6 9.4-7.4 13.9-11.4 2.7-2.4 5.3-4.8 7.9-7.3 5-4.9 6.3-12.5 3.1-18.7s-10.1-9.7-17-8.5c-3.7.6-7.4 1.2-11.1 1.6-5 .5-10.1.9-15.3 1h-4c-96.8-.2-175.2-78.9-175.2-176 0-54.8 24.9-103.7 64.1-136 1-.9 2.1-1.7 3.2-2.6 4-3.2 8.2-6.2 12.5-9 3.1-2 6.3-4 9.6-5.8 6.1-3.5 9.2-10.5 7.7-17.3s-7.3-11.9-14.3-12.5c-3.6-.3-7.1-.5-10.7-.6-2.7-.1-5.5-.1-8.2-.1-3.3 0-6.5.1-9.8.2-2.3.1-4.6.2-6.9.4z"/></svg>
</label>
<input class="md-option" data-md-color-media="(prefers-color-scheme: dark)" data-md-color-scheme="slate" data-md-color-primary="black" data-md-color-accent="indigo" aria-label="Switch to system preference" type="radio" name="__palette" id="__palette_2">
<label class="md-header__button md-icon" title="Switch to system preference" for="__palette_0" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2024 Fonticons, Inc.--><path d="M223.5 32C100 32 0 132.3 0 256s100 224 223.5 224c60.6 0 115.5-24.2 155.8-63.4 5-4.9 6.3-12.5 3.1-18.7s-10.1-9.7-17-8.5c-9.8 1.7-19.8 2.6-30.1 2.6-96.9 0-175.5-78.8-175.5-176 0-65.8 36-123.1 89.3-153.3 6.1-3.5 9.2-10.5 7.7-17.3s-7.3-11.9-14.3-12.5c-6.3-.5-12.6-.8-19-.8z"/></svg>
</label>
</form>
<script>var media,input,key,value,palette=__md_get("__palette");if(palette&&palette.color){"(prefers-color-scheme)"===palette.color.media&&(media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']"),palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent"));for([key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
<label class="md-header__button md-icon" for="__search">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5Z"/></svg>
</label>
<div class="md-search" data-md-component="search" role="dialog">
<label class="md-search__overlay" for="__search"></label>
<div class="md-search__inner" role="search">
<form class="md-search__form" name="search">
<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" required>
<label class="md-search__icon md-icon" for="__search">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5Z"/></svg>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11h12Z"/></svg>
</label>
<nav class="md-search__options" aria-label="Search">
<button type="reset" class="md-search__icon md-icon" title="Clear" aria-label="Clear" tabindex="-1">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12 19 6.41Z"/></svg>
</button>
</nav>
</form>
<div class="md-search__output">
<div class="md-search__scrollwrap" data-md-scrollfix>
<div class="md-search-result" data-md-component="search-result">
<div class="md-search-result__meta">
Initializing search
</div>
<ol class="md-search-result__list" role="presentation"></ol>
</div>
</div>
</div>
</div>
</div>
<div class="md-header__source">
<a href="https://github.com/OmooLab/BioxelNodes" title="Go to repository" class="md-source" data-md-component="source">
<div class="md-source__icon md-icon">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2024 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
</div>
<div class="md-source__repository">
OmooLab/BioxelNodes
</div>
</a>
</div>
</nav>
<nav class="md-tabs" aria-label="Tabs" data-md-component="tabs">
<div class="md-grid">
<ul class="md-tabs__list">
<li class="md-tabs__item md-tabs__item--active">
<a href="." class="md-tabs__link">
BioxelNodes
</a>
</li>
</ul>
</div>
</nav>
</header>
<div class="md-container" data-md-component="container">
<main class="md-main" data-md-component="main">
<div class="md-main__inner md-grid">
<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
<div class="md-sidebar__scrollwrap">
<div class="md-sidebar__inner">
<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">
<img src="assets/logo.png" alt="logo">
</a>
Bioxel Nodes Docs
</label>
<div class="md-nav__source">
<a href="https://github.com/OmooLab/BioxelNodes" title="Go to repository" class="md-source" data-md-component="source">
<div class="md-source__icon md-icon">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2024 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
</div>
<div class="md-source__repository">
OmooLab/BioxelNodes
</div>
</a>
</div>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_1" checked>
<div class="md-nav__link md-nav__container">
<a href="." class="md-nav__link md-nav__link--active">
<span class="md-ellipsis">
BioxelNodes
</span>
</a>
<label class="md-nav__link md-nav__link--active" for="__nav_1" id="__nav_1_label" tabindex="">
<span class="md-nav__icon md-icon"></span>
</label>
</div>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_1_label" aria-expanded="true">
<label class="md-nav__title" for="__nav_1">
<span class="md-nav__icon md-icon"></span>
BioxelNodes
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="getting-started/" class="md-nav__link">
<span class="md-ellipsis">
Getting Started
</span>
</a>
</li>
<li class="md-nav__item">
<a href="features/" class="md-nav__link">
<span class="md-ellipsis">
Features & Options
</span>
</a>
</li>
<li class="md-nav__item">
<a href="nodes/" class="md-nav__link">
<span class="md-ellipsis">
Nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="misc/" class="md-nav__link">
<span class="md-ellipsis">
Future Features
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</div>
</div>
</div>
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
<div class="md-sidebar__scrollwrap">
<div class="md-sidebar__inner">
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
<label class="md-nav__title" for="__toc">
<span class="md-nav__icon md-icon"></span>
Table of contents
</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
<li class="md-nav__item">
<a href="#about" class="md-nav__link">
<span class="md-ellipsis">
About
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#supported-format" class="md-nav__link">
<span class="md-ellipsis">
Supported Format
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#known-limitations" class="md-nav__link">
<span class="md-ellipsis">
Known Limitations
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#to-upgrade-add-on" class="md-nav__link">
<span class="md-ellipsis">
To Upgrade Add-on
</span>
</a>
</li>
</ul>
</nav>
</div>
</div>
</div>
<div class="md-content" data-md-component="content">
<article class="md-content__inner md-typeset">
<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><img alt="gallery" src="assets/gallery.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>
<table>
<thead>
<tr>
<th>Format</th>
<th>EXT</th>
<th>Test</th>
</tr>
</thead>
<tbody>
<tr>
<td>DICOM</td>
<td>.dcm, .DICOM</td>
<td>✅ pass</td>
</tr>
<tr>
<td>BMP</td>
<td>.bmp, .BMP</td>
<td>✅ pass</td>
</tr>
<tr>
<td>JPEG</td>
<td>.jpg, .JPG, .jpeg, .JPEG</td>
<td>✅ pass</td>
</tr>
<tr>
<td>PNG</td>
<td>.png, .PNG</td>
<td>✅ pass</td>
</tr>
<tr>
<td>TIFF</td>
<td>.tif, .TIF, .tiff, .TIFF</td>
<td>✅ pass</td>
</tr>
<tr>
<td>Nifti</td>
<td>.nia, .nii, .nii.gz, .hdr, .img, .img.gz</td>
<td>✅ pass</td>
</tr>
<tr>
<td>Nrrd</td>
<td>.nrrd, .nhdr</td>
<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>
<tr>
<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="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>
</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>
</article>
</div>
<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
</div>
</main>
<footer class="md-footer">
<nav class="md-footer__inner md-grid" aria-label="Footer" >
<a href="getting-started/" class="md-footer__link md-footer__link--next" aria-label="Next: Getting Started">
<div class="md-footer__title">
<span class="md-footer__direction">
Next
</span>
<div class="md-ellipsis">
Getting Started
</div>
</div>
<div class="md-footer__button md-icon">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11H4Z"/></svg>
</div>
</a>
</nav>
<div class="md-footer-meta md-typeset">
<div class="md-footer-meta__inner md-grid">
<div class="md-copyright">
<div class="md-copyright__highlight">
Copyright &copy; 2020 - 2024 Omoolab
</div>
Made with
<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
Material for MkDocs
</a>
</div>
</div>
</div>
</footer>
</div>
<div class="md-dialog" data-md-component="dialog">
<div class="md-dialog__inner md-typeset"></div>
</div>
<script id="__config" type="application/json">{"base": ".", "features": ["header.autohide", "navigation.footer", "navigation.indexes", "navigation.sections", "navigation.tabs", "navigation.tabs.sticky", "content.code.copy", "content.code.select"], "search": "assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>
<script src="assets/javascripts/bundle.5cfa9459.min.js"></script>
</body>
</html>