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<h1 id="sars-cov-2">SARS-Cov-2</h1>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image.png" /></p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-1.png" /></p>
<p>在本教程中,我们将制作 SARS-Cov-2 病毒的结构可视化。请确保您已阅读<a href="step_by_step.md">分步指南</a>以了解插件的基本使用方法,并确保插件版本为 v1.0.2 或更高!</p>
<p>研究数据来自 2020 年 9 月发表在 Cell Press 的论文(<a href="https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4">https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4</a>),作者是清华大学李赛团队。该研究使用冷冻电子断层扫描(cryo-ET)和亚断层图平均(STA)揭示了真实 SARS-CoV-2 病毒的分子组装。以下是该研究的官方视频:</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>"冠状病毒如何将约 30kb 的 RNA 包装到约 80nm 直径的病毒腔内仍然是个谜。RNP 彼此之间是否有序以避免 RNA 缠结、打结或损坏,还是它们参与病毒组装?" 论文中提出了三类组装方式,我们将基于真实的冷冻电镜数据,制作"巢中蛋"形 RNP 组装的可视化。</p>
<h2 id="_1">下载和导入数据</h2>
<p>该研究的数据托管在 EMDB(<a href="https://www.ebi.ac.uk/emdb">https://www.ebi.ac.uk/emdb</a>),SARS-Cov-2 病毒网站是<a href="https://www.ebi.ac.uk/emdb/EMD-30430">这里</a>。打开页面,找到"Download"按钮,选择第一个选项"3D Volume (.map.gz)"。</p>
<p>如果您无法下载数据,可以从这里下载。</p>
<p><a href="https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing">SARS-Cov-2.map</a></p>
<p>下载后,放到任意目录并导入数据。在导入选项中,建议将 Bioxel Size 调整为 5,以减小数据形状,提高计算和渲染速度。如果您对硬件性能有信心,可以保持原始的 2.72 不变。调整 Bioxel Size 后,下方会根据当前的 bioxel size 计算转换后数据的形状。数据量会随着形状增大呈指数增长,可能会导致内存不足(OOM)。</p>
<h2 id="_2">切割病毒</h2>
<p>导入后,您可以通过创建和连接节点并设置参数来获取病毒,如下图所示。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-2.png" /></p>
<p>按下图所示放置灯光和相机。背光是区域光,白色,强度 500W,扩散 90°;在病毒内部放置一个点光源,颜色 <code>FFD08D</code>,强度 5W。相机焦距为 200mm。背景颜色为纯黑色。颜色管理的 Look 为 High Contrast。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-3.png" /></p>
<p>继续编辑节点,接着是"Set Properties"和"Set Color by Ramp 4"节点,这两个节点的参数设置如下图,其中颜色部分,从上到下设置为 <code>E1D0FC</code>(1.0)、<code>FFE42D</code>(0.5)、<code>3793FF</code>(0.5)、<code>FFFF8EC</code>(0.1)(括号中为 alpha 值)。颜色的 alpha 值也会影响密度。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-4.png" /></p>
<p>如果您觉得渲染太慢,请参阅<a href="improve_performance.md">这里</a>获取建议。</p>
<h2 id="rnp">单独为 RNP 着色</h2>
<p>当前的渲染效果很好,但考虑到我的目标是让您清楚看到 RNP 在病毒内部的排列方式,RNP 应该与其他部分用不同颜色着色。那么如何单独为 RNP 着色呢?</p>
<p>首先,我们必须分离 RNP。RNP 的值介于膜和 S 蛋白之间,因此很难分离。好在病毒是球形的,我们可以使用球形切割器将病毒的 RNP 部分与其余部分分离。为此,在容器的几何节点面板菜单中,点击 <strong>Bioxel Nodes &gt; Add a Cutter &gt; Sphere Cutter</strong>,并适当调整新创建的名为"Sphere_Cutter"的球体对象的大小和位置,使其恰好能将病毒内部的 RNP 和膜分离。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-5.png" /></p>
<p>改变"Sphere_Cutter"对象的位置可能会非常卡顿,此时您可以关闭"With Surface"并在 Slice Viewer 模式下操作。满意后,恢复设置。</p>
<p>然后在"Sphere Cutter"节点中打开 Invert,您可以看到相反的结果。这样我们就成功将两者分离了。接下来让我们分别着色,最后用 Join Component 合并。按如下图所示创建和连接节点,其中第二个 Cutter 节点是复制的,Set Color 中的颜色值设置为 <code>FFDDFE</code>(0.5)。如果一切正常,渲染结果应该如下图所示。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-6.png" /></p>
<p>此时,SARS-Cov-2 病毒的渲染完成了!</p>
<h2 id="rnp_1">渲染 RNP 和膜</h2>
<p>写实渲染很棒,但非写实渲染(NPR)在呈现结构信息方面更好。因此,我将使用卡通着色器来渲染 RNP 组装的首尾结构。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-7.png" /></p>
<p>RNP 的轮廓使用 Blender 的线稿(Line Art)功能,但线稿必须基于网格。选择挤出 RNP 的节点(即负责切割出 RNP 的"Cut"节点),右键点击 <strong>Bioxel Nodes &gt; Extract Mesh</strong>。这将为您创建一个 RNP 的新网格对象。</p>
<p>用同样的方式提取膜网格。</p>
<p>膜的病毒值远高于其他部分,因此让我们创建一个新的"Cutout"节点,同样在 ReCenter 之后,但阈值调整为 0.13。Cutout 后,连接到"To Surface"节点并按如下图所示设置参数,注意 Remove Island Threshold 设置为 1000,以便消除小于 1000 pts 的任何碎片。然后选择"To Surface"节点,执行提取网格的操作。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-8.png" /></p>
<p>膜的网格需要切成两半,这可以通过雕刻模式中的 Box Trim 笔刷或布尔修改器来完成。RNP 的网格也可能需要一些修复工作,我清理了一些 RNP 的破损表面。所有网格现在都可以使用了。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-9.png" /></p>
<p>关于线稿,请参阅 Blender Secrets 的视频教程。</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>最后,RNP 超微结构的信息图完成了!</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-1.png" /></p>
<p>如果您按照文档有困难,可以下载项目文件。</p>
<p><a href="https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing">SARS-Cov-2.zip</a></p>
<h2 id="_3">作业</h2>
<p>论文中提供了其他相关数据,您可以尝试可视化它们。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-10.png" /></p>
<p>前往官方 EMDB 网站 https://www.ebi.ac.uk/emdb/,在搜索框中输入 EMD 编号即可获取。</p>
<p>电子显微镜数据银行(EMDB)是一个公共仓库,用于存放冷冻样品的电子显微镜(cryoEM)体积和代表性断层图。如果您想获取其他病毒的数据,只需在搜索框中输入其名称即可。例如,乙型肝炎病毒,在搜索框中输入,然后选择左侧 Sample Type 中的 Virus,下载您需要的数据(最好找到相应的论文来明确数据信息)。</p>
<p><strong>尝试可视化乙型肝炎病毒。</strong></p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-11.png" /></p>
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<h1 id="_1">高级玩法</h1>
<h2 id="_2">切割「结构体」</h2>
<p>「结构体」可以被切割,呈现部分结构,通过 O Cut 系列节点完成。比如按下图添加 <strong>O Cut to Region</strong> 节点并连接,添加任意来自场景的物体作为「区域」,输入到节点:</p>
<p><img alt="" src="../assets/cut-to-region.png" /></p>
<p>适当调整作为「区域」物体的位置旋转,可以看到头骨结构被限制在区域范围内。</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>插件提供快速让物体虚化的功能,在 3D 视图模式下,右键「区域」物体,菜单选择 <strong>Bioxel Nodes &gt; Toggle Phantom</strong></p>
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<p>切割会增加计算量,影响实时性能,勾选 O Layer 的 Resample 来提高性能</p>
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<p><strong>O Cut Small Parts</strong> 节点,是清理神器,能快速把零碎的结构删除,只干净连续的大结构。但是计算特别耗时,注意性能。</p>
<p><img alt="" src="../assets/cut-small-parts.png" /></p>
<p>如果你对几何节点很了解,你也可以通过 <strong>O Cut Structure</strong> 直接定义切割的执行范围,比如下图中,选择切割位置 X 大于 0 的部分。</p>
<p><img alt="" src="../assets/cut-structure.png" /></p>
<h2 id="_3">「结构体」属性设置</h2>
<p>展开 <strong>O Cutout by Threshold</strong> 的 Properties,你可以直接修改各项属性值,但都只能均一设置,我们可以用场类型数据赋予差异。以颜色属性为例,比如直接接入 Position 节点,效果如下:</p>
<p><img alt="" src="../assets/set-color-by-pos.png" /></p>
<p>我们还可以把数据层的值映射为颜色渐变,这里需要用到 <strong>O Scalar Layer to Color</strong> 节点(这类转换功能的节点都在节点菜单,Add &gt; O Bioxel &gt; Utilities 下)。调整如下</p>
<ul>
<li><strong>O Cutout by Threshold</strong>:Threshold 设置为 20</li>
<li><strong>O Scalar Layer to Color</strong>:From Min 和 From Max 分别设置为 20 和 90</li>
</ul>
<p><img alt="" src="../assets/scalar-to-color.png" /></p>
<p>由于软组织的 CT 值小于骨质,当阈值降低,可以看到除了头骨外,附着的软组织也被呈现了出来。<strong>O Scalar Layer to Color</strong> 的 From Min 和 From Max,定义了颜色从 0~1 的取值范围。因此低值的软组织呈现黑色,高值的骨质呈现白色</p>
<p>我们还可以通过 Blender 5.0+ 的 <strong>Closure</strong> 节点来自定义映射方式。比如连接 <strong>Color Ramp</strong> 节点,把属于软组织的黑区,改为暗红色</p>
<p><img alt="" src="../assets/scalar-to-color-ramp.png" /></p>
<p>哒哒!解剖渲染就做好啦👍</p>
<p>其他「结构体」属性也可以按这样的方式调整,除了 <strong>O Scalar Layer to Color</strong>,还有 <strong>O Scalar Layer to Factor</strong> 来转换为 0~1 的单值</p>
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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hi=function(){this.pipeline.reset(),this.pipeline.add(e.hi.trimmer,e.hi.stopWordFilter,e.hi.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hi.stemmer))},e.hi.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿa-zA-Za-zA-Z0-90-9",e.hi.trimmer=e.trimmerSupport.generateTrimmer(e.hi.wordCharacters),e.Pipeline.registerFunction(e.hi.trimmer,"trimmer-hi"),e.hi.stopWordFilter=e.generateStopWordFilter("अत अपना अपनी अपने अभी अंदर आदि आप इत्यादि इन इनका इन्हीं इन्हें इन्हों इस इसका इसकी इसके इसमें इसी इसे उन उनका उनकी उनके उनको उन्हीं उन्हें उन्हों उस उसके उसी उसे एक एवं एस ऐसे और कई कर करता करते करना करने करें कहते कहा का काफ़ी कि कितना किन्हें किन्हों किया किर किस किसी किसे की कुछ कुल के को कोई कौन कौनसा गया घर जब जहाँ जा जितना जिन जिन्हें जिन्हों जिस जिसे जीधर जैसा जैसे जो तक तब तरह तिन तिन्हें तिन्हों तिस तिसे तो था थी थे दबारा दिया दुसरा दूसरे दो द्वारा न नके नहीं ना निहायत नीचे ने पर पहले पूरा पे फिर बनी बही बहुत बाद बाला बिलकुल भी भीतर मगर मानो मे में यदि यह यहाँ यही या यिह ये रखें रहा रहे ऱ्वासा लिए लिये लेकिन व वग़ैरह वर्ग वह वहाँ वहीं वाले वुह वे वो सकता सकते सबसे सभी साथ साबुत साभ सारा से सो संग ही हुआ हुई हुए है हैं हो होता होती होते होना होने".split(" ")),e.hi.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.hi.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var t=i.toString().toLowerCase().replace(/^\s+/,"");return r.cut(t).split("|")},e.Pipeline.registerFunction(e.hi.stemmer,"stemmer-hi"),e.Pipeline.registerFunction(e.hi.stopWordFilter,"stopWordFilter-hi")}});

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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hy=function(){this.pipeline.reset(),this.pipeline.add(e.hy.trimmer,e.hy.stopWordFilter)},e.hy.wordCharacters="[A-Za-z԰-֏ff-ﭏ]",e.hy.trimmer=e.trimmerSupport.generateTrimmer(e.hy.wordCharacters),e.Pipeline.registerFunction(e.hy.trimmer,"trimmer-hy"),e.hy.stopWordFilter=e.generateStopWordFilter("դու և եք էիր էիք հետո նաև նրանք որը վրա է որ պիտի են այս մեջ ն իր ու ի այդ որոնք այն կամ էր մի ես համար այլ իսկ էին ենք հետ ին թ էինք մենք նրա նա դուք եմ էի ըստ որպես ում".split(" ")),e.Pipeline.registerFunction(e.hy.stopWordFilter,"stopWordFilter-hy"),e.hy.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.hy.stemmer,"stemmer-hy")}});

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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.ja=function(){this.pipeline.reset(),this.pipeline.add(e.ja.trimmer,e.ja.stopWordFilter,e.ja.stemmer),r?this.tokenizer=e.ja.tokenizer:(e.tokenizer&&(e.tokenizer=e.ja.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.ja.tokenizer))};var t=new e.TinySegmenter;e.ja.tokenizer=function(i){var n,o,s,p,a,u,m,l,c,f;if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t.toLowerCase()):t.toLowerCase()});for(o=i.toString().toLowerCase().replace(/^\s+/,""),n=o.length-1;n>=0;n--)if(/\S/.test(o.charAt(n))){o=o.substring(0,n+1);break}for(a=[],s=o.length,c=0,l=0;c<=s;c++)if(u=o.charAt(c),m=c-l,u.match(/\s/)||c==s){if(m>0)for(p=t.segment(o.slice(l,c)).filter(function(e){return!!e}),f=l,n=0;n<p.length;n++)r?a.push(new e.Token(p[n],{position:[f,p[n].length],index:a.length})):a.push(p[n]),f+=p[n].length;l=c+1}return a},e.ja.stemmer=function(){return function(e){return e}}(),e.Pipeline.registerFunction(e.ja.stemmer,"stemmer-ja"),e.ja.wordCharacters="一二三四五六七八九十百千万億兆一-龠々〆ヵヶぁ-んァ-ヴーア-ン゙a-zA-Za-zA-Z0-90-9",e.ja.trimmer=e.trimmerSupport.generateTrimmer(e.ja.wordCharacters),e.Pipeline.registerFunction(e.ja.trimmer,"trimmer-ja"),e.ja.stopWordFilter=e.generateStopWordFilter("これ それ あれ この その あの ここ そこ あそこ こちら どこ だれ なに なん 何 私 貴方 貴方方 我々 私達 あの人 あのかた 彼女 彼 です あります おります います は が の に を で え から まで より も どの と し それで しかし".split(" ")),e.Pipeline.registerFunction(e.ja.stopWordFilter,"stopWordFilter-ja"),e.jp=e.ja,e.Pipeline.registerFunction(e.jp.stemmer,"stemmer-jp"),e.Pipeline.registerFunction(e.jp.trimmer,"trimmer-jp"),e.Pipeline.registerFunction(e.jp.stopWordFilter,"stopWordFilter-jp")}});

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module.exports=require("./lunr.ja");

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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.kn=function(){this.pipeline.reset(),this.pipeline.add(e.kn.trimmer,e.kn.stopWordFilter,e.kn.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.kn.stemmer))},e.kn.wordCharacters="ಀ-಄ಅ-ಔಕ-ಹಾ-ೌ಼-ಽೕ-ೖೝ-ೞೠ-ೡೢ-ೣ೤೥೦-೯ೱ-ೳ",e.kn.trimmer=e.trimmerSupport.generateTrimmer(e.kn.wordCharacters),e.Pipeline.registerFunction(e.kn.trimmer,"trimmer-kn"),e.kn.stopWordFilter=e.generateStopWordFilter("ಮತ್ತು ಈ ಒಂದು ರಲ್ಲಿ ಹಾಗೂ ಎಂದು ಅಥವಾ ಇದು ರ ಅವರು ಎಂಬ ಮೇಲೆ ಅವರ ತನ್ನ ಆದರೆ ತಮ್ಮ ನಂತರ ಮೂಲಕ ಹೆಚ್ಚು ನ ಆ ಕೆಲವು ಅನೇಕ ಎರಡು ಹಾಗು ಪ್ರಮುಖ ಇದನ್ನು ಇದರ ಸುಮಾರು ಅದರ ಅದು ಮೊದಲ ಬಗ್ಗೆ ನಲ್ಲಿ ರಂದು ಇತರ ಅತ್ಯಂತ ಹೆಚ್ಚಿನ ಸಹ ಸಾಮಾನ್ಯವಾಗಿ ನೇ ಹಲವಾರು ಹೊಸ ದಿ ಕಡಿಮೆ ಯಾವುದೇ ಹೊಂದಿದೆ ದೊಡ್ಡ ಅನ್ನು ಇವರು ಪ್ರಕಾರ ಇದೆ ಮಾತ್ರ ಕೂಡ ಇಲ್ಲಿ ಎಲ್ಲಾ ವಿವಿಧ ಅದನ್ನು ಹಲವು ರಿಂದ ಕೇವಲ ದ ದಕ್ಷಿಣ ಗೆ ಅವನ ಅತಿ ನೆಯ ಬಹಳ ಕೆಲಸ ಎಲ್ಲ ಪ್ರತಿ ಇತ್ಯಾದಿ ಇವು ಬೇರೆ ಹೀಗೆ ನಡುವೆ ಇದಕ್ಕೆ ಎಸ್ ಇವರ ಮೊದಲು ಶ್ರೀ ಮಾಡುವ ಇದರಲ್ಲಿ ರೀತಿಯ ಮಾಡಿದ ಕಾಲ ಅಲ್ಲಿ ಮಾಡಲು ಅದೇ ಈಗ ಅವು ಗಳು ಎ ಎಂಬುದು ಅವನು ಅಂದರೆ ಅವರಿಗೆ ಇರುವ ವಿಶೇಷ ಮುಂದೆ ಅವುಗಳ ಮುಂತಾದ ಮೂಲ ಬಿ ಮೀ ಒಂದೇ ಇನ್ನೂ ಹೆಚ್ಚಾಗಿ ಮಾಡಿ ಅವರನ್ನು ಇದೇ ಯ ರೀತಿಯಲ್ಲಿ ಜೊತೆ ಅದರಲ್ಲಿ ಮಾಡಿದರು ನಡೆದ ಆಗ ಮತ್ತೆ ಪೂರ್ವ ಆತ ಬಂದ ಯಾವ ಒಟ್ಟು ಇತರೆ ಹಿಂದೆ ಪ್ರಮಾಣದ ಗಳನ್ನು ಕುರಿತು ಯು ಆದ್ದರಿಂದ ಅಲ್ಲದೆ ನಗರದ ಮೇಲಿನ ಏಕೆಂದರೆ ರಷ್ಟು ಎಂಬುದನ್ನು ಬಾರಿ ಎಂದರೆ ಹಿಂದಿನ ಆದರೂ ಆದ ಸಂಬಂಧಿಸಿದ ಮತ್ತೊಂದು ಸಿ ಆತನ ".split(" ")),e.kn.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.kn.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var n=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(n).split("|")},e.Pipeline.registerFunction(e.kn.stemmer,"stemmer-kn"),e.Pipeline.registerFunction(e.kn.stopWordFilter,"stopWordFilter-kn")}});

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!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){e.multiLanguage=function(){for(var t=Array.prototype.slice.call(arguments),i=t.join("-"),r="",n=[],s=[],p=0;p<t.length;++p)"en"==t[p]?(r+="\\w",n.unshift(e.stopWordFilter),n.push(e.stemmer),s.push(e.stemmer)):(r+=e[t[p]].wordCharacters,e[t[p]].stopWordFilter&&n.unshift(e[t[p]].stopWordFilter),e[t[p]].stemmer&&(n.push(e[t[p]].stemmer),s.push(e[t[p]].stemmer)));var o=e.trimmerSupport.generateTrimmer(r);return e.Pipeline.registerFunction(o,"lunr-multi-trimmer-"+i),n.unshift(o),function(){this.pipeline.reset(),this.pipeline.add.apply(this.pipeline,n),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add.apply(this.searchPipeline,s))}}}});

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/*!
* Lunr languages, `Norwegian` language
* https://github.com/MihaiValentin/lunr-languages
*
* Copyright 2014, Mihai Valentin
* http://www.mozilla.org/MPL/
*/
/*!
* based on
* Snowball JavaScript Library v0.3
* http://code.google.com/p/urim/
* http://snowball.tartarus.org/
*
* Copyright 2010, Oleg Mazko
* http://www.mozilla.org/MPL/
*/
!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.no=function(){this.pipeline.reset(),this.pipeline.add(e.no.trimmer,e.no.stopWordFilter,e.no.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.no.stemmer))},e.no.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stA-Za-z",e.no.trimmer=e.trimmerSupport.generateTrimmer(e.no.wordCharacters),e.Pipeline.registerFunction(e.no.trimmer,"trimmer-no"),e.no.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,r=w.cursor+3;if(a=w.limit,0<=r||r<=w.limit){for(s=r;;){if(e=w.cursor,w.in_grouping(d,97,248)){w.cursor=e;break}if(e>=w.limit)return;w.cursor=e+1}for(;!w.out_grouping(d,97,248);){if(w.cursor>=w.limit)return;w.cursor++}a=w.cursor,a<s&&(a=s)}}function i(){var e,r,n;if(w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(m,29),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:n=w.limit-w.cursor,w.in_grouping_b(c,98,122)?w.slice_del():(w.cursor=w.limit-n,w.eq_s_b(1,"k")&&w.out_grouping_b(d,97,248)&&w.slice_del());break;case 3:w.slice_from("er")}}function t(){var e,r=w.limit-w.cursor;w.cursor>=a&&(e=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,w.find_among_b(u,2)?(w.bra=w.cursor,w.limit_backward=e,w.cursor=w.limit-r,w.cursor>w.limit_backward&&(w.cursor--,w.bra=w.cursor,w.slice_del())):w.limit_backward=e)}function o(){var e,r;w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(l,11),e?(w.bra=w.cursor,w.limit_backward=r,1==e&&w.slice_del()):w.limit_backward=r)}var s,a,m=[new r("a",-1,1),new r("e",-1,1),new r("ede",1,1),new r("ande",1,1),new r("ende",1,1),new r("ane",1,1),new r("ene",1,1),new r("hetene",6,1),new r("erte",1,3),new r("en",-1,1),new r("heten",9,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",12,1),new r("s",-1,2),new r("as",14,1),new r("es",14,1),new r("edes",16,1),new r("endes",16,1),new r("enes",16,1),new r("hetenes",19,1),new r("ens",14,1),new r("hetens",21,1),new r("ers",14,1),new r("ets",14,1),new r("et",-1,1),new r("het",25,1),new r("ert",-1,3),new r("ast",-1,1)],u=[new r("dt",-1,-1),new r("vt",-1,-1)],l=[new r("leg",-1,1),new r("eleg",0,1),new r("ig",-1,1),new r("eig",2,1),new r("lig",2,1),new r("elig",4,1),new r("els",-1,1),new r("lov",-1,1),new r("elov",7,1),new r("slov",7,1),new r("hetslov",9,1)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],c=[119,125,149,1],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,i(),w.cursor=w.limit,t(),w.cursor=w.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.no.stemmer,"stemmer-no"),e.no.stopWordFilter=e.generateStopWordFilter("alle at av bare begge ble blei bli blir blitt både båe da de deg dei deim deira deires dem den denne der dere deres det dette di din disse ditt du dykk dykkar då eg ein eit eitt eller elles en enn er et ett etter for fordi fra før ha hadde han hans har hennar henne hennes her hjå ho hoe honom hoss hossen hun hva hvem hver hvilke hvilken hvis hvor hvordan hvorfor i ikke ikkje ikkje ingen ingi inkje inn inni ja jeg kan kom korleis korso kun kunne kva kvar kvarhelst kven kvi kvifor man mange me med medan meg meget mellom men mi min mine mitt mot mykje ned no noe noen noka noko nokon nokor nokre nå når og også om opp oss over på samme seg selv si si sia sidan siden sin sine sitt sjøl skal skulle slik so som som somme somt så sånn til um upp ut uten var vart varte ved vere verte vi vil ville vore vors vort vår være være vært å".split(" ")),e.Pipeline.registerFunction(e.no.stopWordFilter,"stopWordFilter-no")}});

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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sa=function(){this.pipeline.reset(),this.pipeline.add(e.sa.trimmer,e.sa.stopWordFilter,e.sa.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sa.stemmer))},e.sa.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿ꣠-꣱ꣲ-ꣷ꣸-ꣻ꣼-ꣽꣾ-ꣿᆰ0-ᆰ9",e.sa.trimmer=e.trimmerSupport.generateTrimmer(e.sa.wordCharacters),e.Pipeline.registerFunction(e.sa.trimmer,"trimmer-sa"),e.sa.stopWordFilter=e.generateStopWordFilter('तथा अयम्‌ एकम्‌ इत्यस्मिन्‌ तथा तत्‌ वा अयम्‌ इत्यस्य ते आहूत उपरि तेषाम्‌ किन्तु तेषाम्‌ तदा इत्यनेन अधिकः इत्यस्य तत्‌ केचन बहवः द्वि तथा महत्वपूर्णः अयम्‌ अस्य विषये अयं अस्ति तत्‌ प्रथमः विषये इत्युपरि इत्युपरि इतर अधिकतमः अधिकः अपि सामान्यतया ठ इतरेतर नूतनम्‌ द न्यूनम्‌ कश्चित्‌ वा विशालः द सः अस्ति तदनुसारम् तत्र अस्ति केवलम्‌ अपि अत्र सर्वे विविधाः तत्‌ बहवः यतः इदानीम्‌ द दक्षिण इत्यस्मै तस्य उपरि नथ अतीव कार्यम्‌ सर्वे एकैकम्‌ इत्यादि। एते सन्ति उत इत्थम्‌ मध्ये एतदर्थं . स कस्य प्रथमः श्री. करोति अस्मिन् प्रकारः निर्मिता कालः तत्र कर्तुं समान अधुना ते सन्ति स एकः अस्ति सः अर्थात् तेषां कृते . स्थितम् विशेषः अग्रिम तेषाम्‌ समान स्रोतः ख म समान इदानीमपि अधिकतया करोतु ते समान इत्यस्य वीथी सह यस्मिन् कृतवान्‌ धृतः तदा पुनः पूर्वं सः आगतः किम्‌ कुल इतर पुरा मात्रा स विषये उ अतएव अपि नगरस्य उपरि यतः प्रतिशतं कतरः कालः साधनानि भूत तथापि जात सम्बन्धि अन्यत्‌ ग अतः अस्माकं स्वकीयाः अस्माकं इदानीं अन्तः इत्यादयः भवन्तः इत्यादयः एते एताः तस्य अस्य इदम् एते तेषां तेषां तेषां तान् तेषां तेषां तेषां समानः सः एकः च तादृशाः बहवः अन्ये च वदन्ति यत् कियत् कस्मै कस्मै यस्मै यस्मै यस्मै यस्मै न अतिनीचः किन्तु प्रथमं सम्पूर्णतया ततः चिरकालानन्तरं पुस्तकं सम्पूर्णतया अन्तः किन्तु अत्र वा इह इव श्रद्धाय अवशिष्यते परन्तु अन्ये वर्गाः सन्ति ते सन्ति शक्नुवन्ति सर्वे मिलित्वा सर्वे एकत्र"'.split(" ")),e.sa.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.sa.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var i=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(i).split("|")},e.Pipeline.registerFunction(e.sa.stemmer,"stemmer-sa"),e.Pipeline.registerFunction(e.sa.stopWordFilter,"stopWordFilter-sa")}});

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!function(r,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(r.lunr)}(this,function(){return function(r){r.stemmerSupport={Among:function(r,t,i,s){if(this.toCharArray=function(r){for(var t=r.length,i=new Array(t),s=0;s<t;s++)i[s]=r.charCodeAt(s);return i},!r&&""!=r||!t&&0!=t||!i)throw"Bad Among initialisation: s:"+r+", substring_i: "+t+", result: "+i;this.s_size=r.length,this.s=this.toCharArray(r),this.substring_i=t,this.result=i,this.method=s},SnowballProgram:function(){var r;return{bra:0,ket:0,limit:0,cursor:0,limit_backward:0,setCurrent:function(t){r=t,this.cursor=0,this.limit=t.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},getCurrent:function(){var t=r;return r=null,t},in_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},in_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},out_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e>s||e<i)return this.cursor++,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},out_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e>s||e<i)return this.cursor--,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},eq_s:function(t,i){if(this.limit-this.cursor<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor+s)!=i.charCodeAt(s))return!1;return this.cursor+=t,!0},eq_s_b:function(t,i){if(this.cursor-this.limit_backward<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor-t+s)!=i.charCodeAt(s))return!1;return this.cursor-=t,!0},find_among:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=l;m<_.s_size;m++){if(n+l==u){f=-1;break}if(f=r.charCodeAt(n+l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n+_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n+_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},find_among_b:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit_backward,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=_.s_size-1-l;m>=0;m--){if(n-l==u){f=-1;break}if(f=r.charCodeAt(n-1-l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n-_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n-_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},replace_s:function(t,i,s){var e=s.length-(i-t),n=r.substring(0,t),u=r.substring(i);return r=n+s+u,this.limit+=e,this.cursor>=i?this.cursor+=e:this.cursor>t&&(this.cursor=t),e},slice_check:function(){if(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>r.length)throw"faulty slice operation"},slice_from:function(r){this.slice_check(),this.replace_s(this.bra,this.ket,r)},slice_del:function(){this.slice_from("")},insert:function(r,t,i){var s=this.replace_s(r,t,i);r<=this.bra&&(this.bra+=s),r<=this.ket&&(this.ket+=s)},slice_to:function(){return this.slice_check(),r.substring(this.bra,this.ket)},eq_v_b:function(r){return this.eq_s_b(r.length,r)}}}},r.trimmerSupport={generateTrimmer:function(r){var t=new RegExp("^[^"+r+"]+"),i=new RegExp("[^"+r+"]+$");return function(r){return"function"==typeof r.update?r.update(function(r){return r.replace(t,"").replace(i,"")}):r.replace(t,"").replace(i,"")}}}}});

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/*!
* Lunr languages, `Swedish` language
* https://github.com/MihaiValentin/lunr-languages
*
* Copyright 2014, Mihai Valentin
* http://www.mozilla.org/MPL/
*/
/*!
* based on
* Snowball JavaScript Library v0.3
* http://code.google.com/p/urim/
* http://snowball.tartarus.org/
*
* Copyright 2010, Oleg Mazko
* http://www.mozilla.org/MPL/
*/
!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sv=function(){this.pipeline.reset(),this.pipeline.add(e.sv.trimmer,e.sv.stopWordFilter,e.sv.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sv.stemmer))},e.sv.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stA-Za-z",e.sv.trimmer=e.trimmerSupport.generateTrimmer(e.sv.wordCharacters),e.Pipeline.registerFunction(e.sv.trimmer,"trimmer-sv"),e.sv.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,t=new function(){function e(){var e,r=w.cursor+3;if(o=w.limit,0<=r||r<=w.limit){for(a=r;;){if(e=w.cursor,w.in_grouping(l,97,246)){w.cursor=e;break}if(w.cursor=e,w.cursor>=w.limit)return;w.cursor++}for(;!w.out_grouping(l,97,246);){if(w.cursor>=w.limit)return;w.cursor++}o=w.cursor,o<a&&(o=a)}}function t(){var e,r=w.limit_backward;if(w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(u,37),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.in_grouping_b(d,98,121)&&w.slice_del()}}function i(){var e=w.limit_backward;w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.find_among_b(c,7)&&(w.cursor=w.limit,w.ket=w.cursor,w.cursor>w.limit_backward&&(w.bra=--w.cursor,w.slice_del())),w.limit_backward=e)}function s(){var e,r;if(w.cursor>=o){if(r=w.limit_backward,w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(m,5))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.slice_from("lös");break;case 3:w.slice_from("full")}w.limit_backward=r}}var a,o,u=[new r("a",-1,1),new r("arna",0,1),new r("erna",0,1),new r("heterna",2,1),new r("orna",0,1),new r("ad",-1,1),new r("e",-1,1),new r("ade",6,1),new r("ande",6,1),new r("arne",6,1),new r("are",6,1),new r("aste",6,1),new r("en",-1,1),new r("anden",12,1),new r("aren",12,1),new r("heten",12,1),new r("ern",-1,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",18,1),new r("or",-1,1),new r("s",-1,2),new r("as",21,1),new r("arnas",22,1),new r("ernas",22,1),new r("ornas",22,1),new r("es",21,1),new r("ades",26,1),new r("andes",26,1),new r("ens",21,1),new r("arens",29,1),new r("hetens",29,1),new r("erns",21,1),new r("at",-1,1),new r("andet",-1,1),new r("het",-1,1),new r("ast",-1,1)],c=[new r("dd",-1,-1),new r("gd",-1,-1),new r("nn",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1),new r("tt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("els",-1,1),new r("fullt",-1,3),new r("löst",-1,2)],l=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,24,0,32],d=[119,127,149],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,t(),w.cursor=w.limit,i(),w.cursor=w.limit,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.sv.stemmer,"stemmer-sv"),e.sv.stopWordFilter=e.generateStopWordFilter("alla allt att av blev bli blir blivit de dem den denna deras dess dessa det detta dig din dina ditt du där då efter ej eller en er era ert ett från för ha hade han hans har henne hennes hon honom hur här i icke ingen inom inte jag ju kan kunde man med mellan men mig min mina mitt mot mycket ni nu när någon något några och om oss på samma sedan sig sin sina sitta själv skulle som så sådan sådana sådant till under upp ut utan vad var vara varför varit varje vars vart vem vi vid vilka vilkas vilken vilket vår våra vårt än är åt över".split(" ")),e.Pipeline.registerFunction(e.sv.stopWordFilter,"stopWordFilter-sv")}});

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!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ta=function(){this.pipeline.reset(),this.pipeline.add(e.ta.trimmer,e.ta.stopWordFilter,e.ta.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.ta.stemmer))},e.ta.wordCharacters="஀-உஊ-ஏஐ-ஙச-ட஠-னப-யர-ஹ஺-ிீ-௉ொ-௏ௐ-௙௚-௟௠-௩௪-௯௰-௹௺-௿a-zA-Za-zA-Z0-90-9",e.ta.trimmer=e.trimmerSupport.generateTrimmer(e.ta.wordCharacters),e.Pipeline.registerFunction(e.ta.trimmer,"trimmer-ta"),e.ta.stopWordFilter=e.generateStopWordFilter("அங்கு அங்கே அது அதை அந்த அவர் அவர்கள் அவள் அவன் அவை ஆக ஆகவே ஆகையால் ஆதலால் ஆதலினால் ஆனாலும் ஆனால் இங்கு இங்கே இது இதை இந்த இப்படி இவர் இவர்கள் இவள் இவன் இவை இவ்வளவு உனக்கு உனது உன் உன்னால் எங்கு எங்கே எது எதை எந்த எப்படி எவர் எவர்கள் எவள் எவன் எவை எவ்வளவு எனக்கு எனது எனவே என் என்ன என்னால் ஏது ஏன் தனது தன்னால் தானே தான் நாங்கள் நாம் நான் நீ நீங்கள்".split(" ")),e.ta.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.ta.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.ta.stemmer,"stemmer-ta"),e.Pipeline.registerFunction(e.ta.stopWordFilter,"stopWordFilter-ta")}});

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!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.te=function(){this.pipeline.reset(),this.pipeline.add(e.te.trimmer,e.te.stopWordFilter,e.te.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.te.stemmer))},e.te.wordCharacters="ఀ-ఄఅ-ఔక-హా-ౌౕ-ౖౘ-ౚౠ-ౡౢ-ౣ౦-౯౸-౿఼ఽ్ౝ౷౤౥",e.te.trimmer=e.trimmerSupport.generateTrimmer(e.te.wordCharacters),e.Pipeline.registerFunction(e.te.trimmer,"trimmer-te"),e.te.stopWordFilter=e.generateStopWordFilter("అందరూ అందుబాటులో అడగండి అడగడం అడ్డంగా అనుగుణంగా అనుమతించు అనుమతిస్తుంది అయితే ఇప్పటికే ఉన్నారు ఎక్కడైనా ఎప్పుడు ఎవరైనా ఎవరో ఏ ఏదైనా ఏమైనప్పటికి ఒక ఒకరు కనిపిస్తాయి కాదు కూడా గా గురించి చుట్టూ చేయగలిగింది తగిన తర్వాత దాదాపు దూరంగా నిజంగా పై ప్రకారం ప్రక్కన మధ్య మరియు మరొక మళ్ళీ మాత్రమే మెచ్చుకో వద్ద వెంట వేరుగా వ్యతిరేకంగా సంబంధం".split(" ")),e.te.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.te.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.te.stemmer,"stemmer-te"),e.Pipeline.registerFunction(e.te.stopWordFilter,"stopWordFilter-te")}});

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!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.th=function(){this.pipeline.reset(),this.pipeline.add(e.th.trimmer),r?this.tokenizer=e.th.tokenizer:(e.tokenizer&&(e.tokenizer=e.th.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.th.tokenizer))},e.th.wordCharacters="[฀-๿]",e.th.trimmer=e.trimmerSupport.generateTrimmer(e.th.wordCharacters),e.Pipeline.registerFunction(e.th.trimmer,"trimmer-th");var t=e.wordcut;t.init(),e.th.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t):t});var n=i.toString().replace(/^\s+/,"");return t.cut(n).split("|")}}});

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TinySegmenter.prototype.ctype_ = function(str) {
for (var i in this.chartype_) {
if (str.match(this.chartype_[i][0])) {
return this.chartype_[i][1];
}
}
return "O";
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TinySegmenter.prototype.ts_ = function(v) {
if (v) { return v; }
return 0;
}
TinySegmenter.prototype.segment = function(input) {
if (input == null || input == undefined || input == "") {
return [];
}
var result = [];
var seg = ["B3","B2","B1"];
var ctype = ["O","O","O"];
var o = input.split("");
for (i = 0; i < o.length; ++i) {
seg.push(o[i]);
ctype.push(this.ctype_(o[i]))
}
seg.push("E1");
seg.push("E2");
seg.push("E3");
ctype.push("O");
ctype.push("O");
ctype.push("O");
var word = seg[3];
var p1 = "U";
var p2 = "U";
var p3 = "U";
for (var i = 4; i < seg.length - 3; ++i) {
var score = this.BIAS__;
var w1 = seg[i-3];
var w2 = seg[i-2];
var w3 = seg[i-1];
var w4 = seg[i];
var w5 = seg[i+1];
var w6 = seg[i+2];
var c1 = ctype[i-3];
var c2 = ctype[i-2];
var c3 = ctype[i-1];
var c4 = ctype[i];
var c5 = ctype[i+1];
var c6 = ctype[i+2];
score += this.ts_(this.UP1__[p1]);
score += this.ts_(this.UP2__[p2]);
score += this.ts_(this.UP3__[p3]);
score += this.ts_(this.BP1__[p1 + p2]);
score += this.ts_(this.BP2__[p2 + p3]);
score += this.ts_(this.UW1__[w1]);
score += this.ts_(this.UW2__[w2]);
score += this.ts_(this.UW3__[w3]);
score += this.ts_(this.UW4__[w4]);
score += this.ts_(this.UW5__[w5]);
score += this.ts_(this.UW6__[w6]);
score += this.ts_(this.BW1__[w2 + w3]);
score += this.ts_(this.BW2__[w3 + w4]);
score += this.ts_(this.BW3__[w4 + w5]);
score += this.ts_(this.TW1__[w1 + w2 + w3]);
score += this.ts_(this.TW2__[w2 + w3 + w4]);
score += this.ts_(this.TW3__[w3 + w4 + w5]);
score += this.ts_(this.TW4__[w4 + w5 + w6]);
score += this.ts_(this.UC1__[c1]);
score += this.ts_(this.UC2__[c2]);
score += this.ts_(this.UC3__[c3]);
score += this.ts_(this.UC4__[c4]);
score += this.ts_(this.UC5__[c5]);
score += this.ts_(this.UC6__[c6]);
score += this.ts_(this.BC1__[c2 + c3]);
score += this.ts_(this.BC2__[c3 + c4]);
score += this.ts_(this.BC3__[c4 + c5]);
score += this.ts_(this.TC1__[c1 + c2 + c3]);
score += this.ts_(this.TC2__[c2 + c3 + c4]);
score += this.ts_(this.TC3__[c3 + c4 + c5]);
score += this.ts_(this.TC4__[c4 + c5 + c6]);
// score += this.ts_(this.TC5__[c4 + c5 + c6]);
score += this.ts_(this.UQ1__[p1 + c1]);
score += this.ts_(this.UQ2__[p2 + c2]);
score += this.ts_(this.UQ3__[p3 + c3]);
score += this.ts_(this.BQ1__[p2 + c2 + c3]);
score += this.ts_(this.BQ2__[p2 + c3 + c4]);
score += this.ts_(this.BQ3__[p3 + c2 + c3]);
score += this.ts_(this.BQ4__[p3 + c3 + c4]);
score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]);
score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]);
score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]);
score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]);
var p = "O";
if (score > 0) {
result.push(word);
word = "";
p = "B";
}
p1 = p2;
p2 = p3;
p3 = p;
word += seg[i];
}
result.push(word);
return result;
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<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://docs.omoolab.xyz/bioxelnodes/2.0.x/basics/">
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<link rel="next" href="../advanced/">
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<meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.30">
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1. 下载数据
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2. 导入为「数据层」
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3. 提取并渲染「结构体」
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4. 另存数据缓存(可选)
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<h1 id="_1">入门</h1>
<h2 id="1">1. 下载数据</h2>
<p>下载并解压到文件夹中 <a href="https://drive.google.com/file/d/1bBGpt5pQ0evr-0-f4KDNRnKPoUYj2bJ-/view?usp=drive_link">VHP_M_CT_Head.zip</a><br />
数据来自 <a href="https://www.nlm.nih.gov/research/visible/visible_human.html">Visible Human Project (VHP)</a>这是一个男性头部的 CT 扫描图像</p>
<h2 id="2">2. 导入为「数据层」</h2>
<p>给立方体添加几何节点,并打开几何节点界面侧边栏。切换到 Bioxel Nodes 分页(1),点击 Import Data 按钮(2),在文件选择对话框中,选择数据文件夹中任意一个<code>.dcm</code>文件(3),点击 Import Data 按钮(4)</p>
<p><img alt="" src="../assets/import-data.png" /></p>
<p>依次会弹出两个对话框,都点击 OK 按钮,等待数据导入(可查看 Blender 界面右下角状态栏的进度条)成功后可以看到 Bioxel Nodes 侧边栏多了数据预览画面。点击下方的 Add 按钮(1),鼠标移动到节点面板,放置 <strong>O Layer</strong> 节点(2)</p>
<p><img alt="" src="../assets/add-o-layer.png" /></p>
<p>数据的导入就完成啦👍</p>
<p>数据缓存在主目录里,以「数据层(Layer)」形式添加在 Blender 文件中,「数据层」通过 <strong>O Layer</strong> 节点装载到几何节点。它们的关系如下:</p>
<p>数据缓存 -&gt; 数据层 -&gt; O Layer</p>
<h2 id="3">3. 提取并渲染「结构体」</h2>
<p>对「数据层」的操作通过 O Bioxel 系列几何节点完成。</p>
<p>我们需要额外两个节点,<strong>O Cutout by Threshold</strong> 和 <strong>O Realize Structure</strong> 节点(它们都在节点菜单,Add &gt; O Bioxel &gt; Structure 下),并按下图连接:</p>
<p><img alt="" src="../assets/connect-nodes.png" /></p>
<p>如果成功,可以看到视图中出现了灰色的头部。接下来我们调整节点参数:</p>
<ul>
<li><strong>O Layer</strong>:勾选 Center,取消 Resample</li>
<li><strong>O Cutout by Threshold</strong>:Threshold 设置为 90</li>
<li><strong>O Realize Structure</strong>:Density 设置为 40,勾选 Surface</li>
</ul>
<p>调整物体转向、灯位置,设置渲染器为 Cycles,最终效果如下图:</p>
<p><img alt="" src="../assets/adjust-nodes.png" /></p>
<p>这样我们就完成了头部 CT 数据的体积渲染👍</p>
<p>简单捋一下执行逻辑,「数据层」先被剪出(Cutout)为「结构体」。「结构体」顾名思义就是负责储存生物组织结构的对象,但它本身数据类型是体积,并不能直接被看到。需要 <strong>O Realize Structure</strong> 来呈现「结构体」</p>
<h2 id="4">4. 另存数据缓存(可选)</h2>
<p>由于数据缓存只是以链接形式保存在 Blender 文件中,所以只传递 Blender 文件给其他设备,会导致「数据层」遗失缓存。点击 Bioxel Nodes 分页中 Save 按钮,选择数据缓存的另存位置来管理缓存资源。</p>
<p>就像图片一样,传递时把数据缓存和 Blender 文件一起发送。</p>
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<h1 id="_1">支持的格式</h1>
<p>迫不及待想使用自己的数据来体验插件了?以下是当前支持的格式列表。</p>
<table>
<thead>
<tr>
<th>格式</th>
<th>扩展名</th>
</tr>
</thead>
<tbody>
<tr>
<td>DICOM</td>
<td>.dcm, .DCM, .DICOM, .ima, .IMA</td>
</tr>
<tr>
<td>BMP</td>
<td>.bmp, .BMP</td>
</tr>
<tr>
<td>JPEG</td>
<td>.jpg, .JPG, .jpeg, .JPEG</td>
</tr>
<tr>
<td>PNG</td>
<td>.png, .PNG</td>
</tr>
<tr>
<td>TIFF</td>
<td>.tif, .TIF, .tiff, .TIFF</td>
</tr>
<tr>
<td>Nifti</td>
<td>.nia, .nii, .nii.gz, .hdr, .img, .img.gz</td>
</tr>
<tr>
<td>Nrrd</td>
<td>.nrrd, .nhdr</td>
</tr>
<tr>
<td>HDF5</td>
<td>.hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5</td>
</tr>
<tr>
<td>OME</td>
<td>.ome.tiff, .ome.tif</td>
</tr>
<tr>
<td>MRC</td>
<td>.mrc, .mrc.gz, .map, .map.gz</td>
</tr>
</tbody>
</table>
<p>尽管我尽了最大努力,仍然无法实现对所有体数据格式的完美支持,我将持续努力改进。</p>
<h2 id="_2">公开数据库</h2>
<p>如果您没有体数据,可以从一些公开数据库下载。</p>
<p><strong>请注意,虽然它们是公开的且可供下载,但并不意味着您可以将其用于任何目的!请务必查看网站上的可用范围说明。</strong></p>
<table>
<thead>
<tr>
<th>来源</th>
<th>对象</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://www.morphosource.org/">MorphoSource</a></td>
<td>开放研究数据</td>
</tr>
<tr>
<td><a href="https://datadryad.org">Dryad</a></td>
<td>开放研究数据</td>
</tr>
<tr>
<td><a href="http://cellimagelibrary.org/home">Cell Image Library</a></td>
<td>细胞</td>
</tr>
<tr>
<td><a href="https://openorganelle.janelia.org/datasets">OpenOrganelle</a></td>
<td>细胞</td>
</tr>
<tr>
<td><a href="https://www.allencell.org/3d-cell-viewer.html">Allen Cell Explorer</a></td>
<td>细胞</td>
</tr>
<tr>
<td><a href="https://www.ebi.ac.uk/emdb/">EMDB</a></td>
<td>蛋白质、病毒</td>
</tr>
<tr>
<td><a href="https://portal.imaging.datacommons.cancer.gov/explore/">IDC</a></td>
<td>医学图像</td>
</tr>
<tr>
<td><a href="https://www.embodi3d.com/files/category/37-medical-scans/">Embodi3D</a></td>
<td>医学图像</td>
</tr>
<tr>
<td><a href="https://github.com/sfikas/medical-imaging-datasets">Github</a></td>
<td>医学图像</td>
</tr>
<tr>
<td><a href="https://nhsx.github.io/open-source-imaging-data-sets/">NIHR</a></td>
<td>医学图像</td>
</tr>
<tr>
<td><a href="http://medicaldecathlon.com/">Medical Segmentation Decathlon</a></td>
<td>医学图像</td>
</tr>
<tr>
<td><a href="https://www.nih.gov/research/visible/visible_human.html">Visible Human Project</a></td>
<td>医学图像</td>
</tr>
</tbody>
</table>
</article>
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<h1 id="sars-cov-2">SARS-Cov-2</h1>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image.png" /></p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-1.png" /></p>
<p>In this tutorial, we'll make a structural visualzation of the SARS-Cov-2 Virus. Please see <a href="step_by_step.md">step by step</a> to make sure you have a basic understanding of how to use the addon, and make sure the addon version is v1.0.2 or higher!</p>
<p>Research data is from paper published in September 2020 in Cell Press (<a href="https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4">https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4</a>) by Li Sai team at Tsinghua University. This research revealed the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Here is an official video of this study</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>"It remains enigmatic how coronaviruses pack the ∼30-kb RNA into the ∼80-nm-diameter viral lumen. Are the RNPs ordered relative to each other to avoid RNA entangling, knotting, or even damage or are they involved in virus assembly?" Three assembly classes were proposed in the paper, we will make a visualzation of the "eggs-in-a-nest"-shaped RNPs assembly, based on real cryo-ET data.</p>
<h2 id="download-and-import-data">Download and import data</h2>
<p>The data of this research is hosted on EMDB (<a href="https://www.ebi.ac.uk/emdb">https://www.ebi.ac.uk/emdb</a>), and the website of SARS-Cov-2 virus is <a href="https://www.ebi.ac.uk/emdb/EMD-30430">here</a>. Open the page, find "Download" button and select the first selection "3D Volume (.map.gz)".</p>
<p>In case you can't download data, you can download here.</p>
<p><a href="https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing">SARS-Cov-2.map</a></p>
<p>After downloading, put it into any directory and import the data. In the import options, it is recommended to adjust the Bioxel Size to 5, in order to reduce the shape of the data to increase the speed of calculation and rendering. If you are confident in the performance of your hardware, you can leave the original 2.72 unchanged. After adjusting the Bioxel Size, the shape of the converted data will be calculated below based on the current bioxel size. The amount of data will increase exponentially with larger shape, and may result in OOM (out of memory).</p>
<h2 id="cutout-the-virus">Cutout the Virus</h2>
<p>After importing, you can get the virus by creating and connecting nodes and setting parameters as shown below</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-2.png" /></p>
<p>Place the light and the camera in the way as below. The backlight is a area light, color white, intensity 500W, spread 90°, and inside the virus, place a point light, color <code>FFD08D</code>, intensity 5W. Camera focal length is 200 mm. the background color is pure black. The Look of the color management is High Contrast.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-3.png" /></p>
<p>Continue editing the node, followed by "Set Properies" and "Set Color by Ramp 4" node, the parameters of these two nodes are set as shown in the figure, where the color part, from top to bottom, is set to <code>E1D0FC</code> (1.0), <code>FFE42D</code> (0.5), <code>3793FF</code> (0.5), <code>FFFF8EC</code> (0.1) (alpha value in parentheses). Color alpha also affects density.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-4.png" /></p>
<p>If you feel that rendering is too slow, see <a href="improve_performance.md">here</a> for suggestions</p>
<h2 id="color-the-rnps-alone">Color the RNPs alone</h2>
<p>The current rendering is pretty good, but considering that my goal is to make it clear how the RNPs are arranged within the virus, the RNPs should be colored differently than the others. So how to color the RNPs alone?</p>
<p>First of all, we have to separate the RNPs. The value of RNPs is between the membrane and S protein, so it is very difficult to separate. The good thing is that the virus is spherical, we can separate the RNPs part of the virus from the rest by using a sphere cutter. To do so, in the Geometry Nodes panel menu of the container, click <strong>Bioxel Nodes &gt; Add a Cutter &gt; Sphere Cutter</strong>, and adjust the scale and position of the newly created sphere object named "Sphere_Cutter" appropriately, so that it can just separate the internal RNPs and membrane of the virus.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-5.png" /></p>
<p>The process of changing the position of the "Sphere_Cutter" object can be very laggy, then you can turn off "With Surface" and do it in Slice Viewer mode. Once you are happy with it, you can restore the settings.</p>
<p>Then we turn on Invert in the "Sphere Cutter" node and you can see the opposite result. This way we've managed to separate the two, next let's color them separately and finally merge them with Join Component. Create and join the nodes as shown below, where the second Cutter node is copied and the color value in Set Color is <code>FFDDFE</code> (0.5). If all is well, the rendering should look like below.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-6.png" /></p>
<p>At this point, the rendering of a SARS-Cov-2 virus is complete!</p>
<h2 id="render-rnps-and-membranes">Render RNPs and Membranes</h2>
<p>Realistic rendering is great, but Non-photorealistic rendering (NPR) is better for presenting structural information. So I will render ultrastructure of the RNPs assembly with toon shader.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-7.png" /></p>
<p>The silhouettes of RNPs uses Blender's Line Art feature, but Line Art must be based on a mesh. Select the nodes that are extruding the RNPs (i.e., the "Cut" nodes that are in charge of cutting out the RNPs), and right-click, click <strong>Bioxel Nodes &gt; Extract Mesh</strong>. This gives you a new mesh object of the RNPs.</p>
<p>Extract the membrane mesh in the same way.</p>
<p>The membrane has a much higher value than the rest of the virus, so let's create a new "Cutout" node, also after the ReCenter, but with the threshold adjusted to 0.13. After the Cutout, connect to the "To Surface" node and parameterize it as shown in the figure, noting that the Remove Island Threshold is set to 1000 so that any fragments smaller than 1000 pts be eliminated. Then select the "To Surface" node, and perform the operation of extracting the mesh.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-8.png" /></p>
<p>The mesh of the membrane needs to be cut in half, this can be done with the Box Trim brush in sculpt mode or with the Boolean modifier. the mesh of the RNPs may also need some repair work, I cleaned up some of the broken surfaces of the RNPs. all the meshes are now ready to be used.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-9.png" /></p>
<p>For Line Art, please see the video tutorial from Blender Secrets.</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>Finally, an infographic on the ultrastructure of RNPs is done!</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-1.png" /></p>
<p>If you have trouble following the docs, you can download the project files.</p>
<p><a href="https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing">SARS-Cov-2.zip</a></p>
<h2 id="homework">Homework</h2>
<p>Other data relevant to the study are provided in the paper, you could try visualizing them.</p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-10.png" /></p>
<p>Go to the official EMDB website https://www.ebi.ac.uk/emdb/ and enter the EMD number in the search box to get them.</p>
<p>The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. If you want to get data on other virus, just enter their name in the search box. For example, hepatitis B virus, enter it into the search box, then select Virus in the Sample Type on the left side, and download the data you need (it is better to find the corresponding paper to clarify the data information).</p>
<p><strong>Try to visualize hepatitis B virus.</strong></p>
<p><img alt="alt text" src="../../assets/SARS-Cov-2/image-11.png" /></p>
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<h1 id="advanced-usage">Advanced Usage</h1>
<h2 id="cut-structure">Cut "Structure"</h2>
<p>"Structure" can be cut to show partial structure, accomplished through the O Cut series nodes. For example, add the <strong>O Cut to Region</strong> node as shown below and connect it. Add any object from the scene as the "Region", and input it into the node:</p>
<p><img alt="" src="../../assets/cut-to-region.png" /></p>
<p>By properly adjusting the position and rotation of the "Region" object, you can see that the skull structure is confined within the region.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The add-on provides a function to quickly make objects phantom. In 3D Viewport mode, right-click the "Region" object and select <strong>Bioxel Nodes &gt; Toggle Phantom</strong> from the menu.</p>
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<p class="admonition-title">Warning</p>
<p>Cutting increases computation and affects real-time performance. Check Resample on O Layer to improve performance.</p>
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<p><strong>O Cut Small Parts</strong> node is a cleanup tool that quickly removes scattered fragments and keeps only clean, continuous large structures. However, the computation is particularly time-consuming, so be aware of performance.</p>
<p><img alt="" src="../../assets/cut-small-parts.png" /></p>
<p>If you are familiar with geometry nodes, you can also directly define the cutting execution range through <strong>O Cut Structure</strong>. For example, in the image below, select the part where the cutting position X is greater than 0.</p>
<p><img alt="" src="../../assets/cut-structure.png" /></p>
<h2 id="structure-property-settings">Structure Property Settings</h2>
<p>Expand the Properties of <strong>O Cutout by Threshold</strong>, where you can directly modify various property values, but they can only be set uniformly. We can use field-type data to assign differences. Take the color property as an example: for instance, connecting a Position node directly produces the effect shown below:</p>
<p><img alt="" src="../../assets/set-color-by-pos.png" /></p>
<p>We can also map layer values to color gradients, which requires the <strong>O Scalar Layer to Color</strong> node (such conversion function nodes are all under Add &gt; O Bioxel &gt; Utilities in the node menu). Adjust as follows:</p>
<ul>
<li><strong>O Cutout by Threshold</strong>: Set Threshold to 20</li>
<li><strong>O Scalar Layer to Color</strong>: Set From Min and From Max to 20 and 90 respectively</li>
</ul>
<p><img alt="" src="../../assets/scalar-to-color.png" /></p>
<p>Since soft tissue CT values are lower than bone tissue, when the threshold is lowered, you can see that in addition to the skull, the attached soft tissue is also presented. The From Min and From Max of <strong>O Scalar Layer to Color</strong> define the color mapping range from 0 to 1. Therefore, low-value soft tissue appears black, and high-value bone tissue appears white.</p>
<p>We can also customize the mapping method through the <strong>Closure</strong> node in Blender 5.0+. For example, connect a <strong>Color Ramp</strong> node to change the black area belonging to soft tissue to dark red:</p>
<p><img alt="" src="../../assets/scalar-to-color-ramp.png" /></p>
<p>Ta-da! The anatomical rendering is done!</p>
<p>Other "Structure" properties can also be adjusted in this way. In addition to <strong>O Scalar Layer to Color</strong>, there is also <strong>O Scalar Layer to Factor</strong> to convert to a single value from 0 to 1.</p>
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<h1 id="bacsic-usage">Bacsic Usage</h1>
<h2 id="1-download-data">1. Download Data</h2>
<p>Download and unzip <a href="https://drive.google.com/file/d/1bBGpt5pQ0evr-0-f4KDNRnKPoUYj2bJ-/view?usp=drive_link">VHP_M_CT_Head.zip</a> to a folder.
The data comes from <a href="https://www.nlm.nih.gov/research/visible/visible_human.html">Visible Human Project (VHP)</a>, which is a CT scan image of a male head.</p>
<h2 id="2-import-as-layer">2. Import as "Layer"</h2>
<p>Add a geometry node to the cube and open the geometry node interface sidebar. Switch to the Bioxel Nodes tab (1), click the Import Data button (2), and in the file selection dialog, choose any <code>.dcm</code> file from the data folder (3), then click the Import Data button (4).</p>
<p><img alt="" src="../../assets/import-data.png" /></p>
<p>Two dialogs will pop up in sequence, click OK for both. Wait for the data import (you can check the progress bar in the Blender interface status bar at the bottom right). After success, you will see a data preview in the Bioxel Nodes sidebar. Click the Add button at the bottom (1), move the mouse to the node panel, and place the <strong>O Layer</strong> node (2).</p>
<p><img alt="" src="../../assets/add-o-layer.png" /></p>
<p>The data import is complete!</p>
<p>The data cache is saved as a link in the Blender file in the form of a "Layer", and the "Layer" is loaded into geometry nodes through the <strong>O Layer</strong> node. Their relationship is as follows:</p>
<p>Data Cache -&gt; Layer -&gt; O Layer</p>
<h2 id="3-extract-and-render-structure">3. Extract and Render "Structure"</h2>
<p>Operations on "Layer" are done through the O Bioxel series geometry nodes.</p>
<p>We need two additional nodes: <strong>O Cutout by Threshold</strong> and <strong>O Realize Structure</strong> nodes (both are in the node menu under Add &gt; O Bioxel &gt; Structure), and connect them as shown below:</p>
<p><img alt="" src="../../assets/connect-nodes.png" /></p>
<p>If successful, you will see a gray head appear in the viewport. Now let's adjust the node parameters:</p>
<ul>
<li><strong>O Layer</strong>: Check Center, uncheck Resample</li>
<li><strong>O Cutout by Threshold</strong>: Set Threshold to 90</li>
<li><strong>O Realize Structure</strong>: Set Density to 40, check Surface</li>
</ul>
<p>Rotate the object, adjust the light position, set the renderer to Cycles, and the final effect is shown below:</p>
<p><img alt="" src="../../assets/adjust-nodes.png" /></p>
<p>Now we have completed the volumetric rendering of the head CT data!</p>
<p>Let's review the execution logic: First, cutout the "Structure" from the "Layer". As the name suggests, "Structure" is responsible for storing biological tissue structure, but its data type is volumetric and cannot be seen directly. It requires <strong>O Realize Structure</strong> to present the "Structure".</p>
<h2 id="4-save-data-cache-optional">4. Save Data Cache (Optional)</h2>
<p>Since the data cache is only saved as a link in the Blender file, passing only the Blender file to other devices will cause the "Layer" to lose its cache. Click the Save button in the Bioxel Nodes tab, and select a location to save the data cache to manage the cache resource.</p>
<p>Just like images, when sharing, send both the data cache and the Blender file together.</p>
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<h1 id="support-format">Support Format</h1>
<p>Can't wait to play with the addon using your own data? Here's a list of the formats currently supported.</p>
<table>
<thead>
<tr>
<th>Format</th>
<th>EXT</th>
</tr>
</thead>
<tbody>
<tr>
<td>DICOM</td>
<td>.dcm, .DCM, .DICOM, .ima, .IMA</td>
</tr>
<tr>
<td>BMP</td>
<td>.bmp, .BMP</td>
</tr>
<tr>
<td>JPEG</td>
<td>.jpg, .JPG, .jpeg, .JPEG</td>
</tr>
<tr>
<td>PNG</td>
<td>.png, .PNG</td>
</tr>
<tr>
<td>TIFF</td>
<td>.tif, .TIF, .tiff, .TIFF</td>
</tr>
<tr>
<td>Nifti</td>
<td>.nia, .nii, .nii.gz, .hdr, .img, .img.gz</td>
</tr>
<tr>
<td>Nrrd</td>
<td>.nrrd, .nhdr</td>
</tr>
<tr>
<td>HDF5</td>
<td>.hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5</td>
</tr>
<tr>
<td>OME</td>
<td>.ome.tiff, .ome.tif</td>
</tr>
<tr>
<td>MRC</td>
<td>.mrc, .mrc.gz, .map, .map.gz</td>
</tr>
</tbody>
</table>
<p>Despite my best efforts, I still can't achieve perfect support for all volumetric data formats, and I will continue to work on this.</p>
<h2 id="open-databases">Open Databases</h2>
<p>If you don't have volumetric data, then you can download from some open databases.</p>
<p><strong>Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website.</strong></p>
<table>
<thead>
<tr>
<th>Source</th>
<th>Object</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://www.morphosource.org/">MorphoSource</a></td>
<td>Open Research Data</td>
</tr>
<tr>
<td><a href="https://datadryad.org">Dryad</a></td>
<td>Open Research Data</td>
</tr>
<tr>
<td><a href="http://cellimagelibrary.org/home">Cell Image Library</a></td>
<td>Cells</td>
</tr>
<tr>
<td><a href="https://openorganelle.janelia.org/datasets">OpenOrganelle</a></td>
<td>Cells</td>
</tr>
<tr>
<td><a href="https://www.allencell.org/3d-cell-viewer.html">Allen Cell Explorer</a></td>
<td>Cells</td>
</tr>
<tr>
<td><a href="https://www.ebi.ac.uk/emdb/">EMDB</a></td>
<td>Protein, Viruses</td>
</tr>
<tr>
<td><a href="https://portal.imaging.datacommons.cancer.gov/explore/">IDC</a></td>
<td>Medical Images</td>
</tr>
<tr>
<td><a href="https://www.embodi3d.com/files/category/37-medical-scans/">Embodi3D</a></td>
<td>Medical Images</td>
</tr>
<tr>
<td><a href="https://github.com/sfikas/medical-imaging-datasets">Github</a></td>
<td>Medical Images</td>
</tr>
<tr>
<td><a href="https://nhsx.github.io/open-source-imaging-data-sets/">NIHR</a></td>
<td>Medical Images</td>
</tr>
<tr>
<td><a href="http://medicaldecathlon.com/">Medical Segmentation Decathlon</a></td>
<td>Medical Images</td>
</tr>
<tr>
<td><a href="https://www.nlm.nih.gov/research/visible/visible_human.html">Visible Human Project</a></td>
<td>Medical Images</td>
</tr>
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<h2 id="nothing-in-the-scene-when-rendering">Nothing in the scene when rendering?</h2>
<p>If you're using the Cycles renderer with GPU, make sure your GPU supports "Optix", as Bioxel Nodes relies on OSL (Open shader language) for volumetric rendering, otherwise you'll have to use the CPU for rendering.</p>
<p>If you're using the EEVEE renderer, this issue is due to EEVEE not loading shaders for some unknown reason, save the file and restart Blender to fix it.</p>
<h2 id="after-updating-the-addon-the-nodes-in-the-file-have-turned-red">After updating the addon, the nodes in the file have turned red?</h2>
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<p><strong>v2.0.x has been released, supporting only Blender 5.0+. The usage is completely different from before and is not compatible with old version files. See http://docs.omoolab.xyz/bioxelnodes/2.0.x/en/basics/</strong></p>
<h1 id="bioxel-nodes">Bioxel Nodes</h1>
<p><a href="https://blender.org/"><img alt="For Blender" src="https://img.shields.io/badge/Blender-orange?style=for-the-badge&amp;logo=blender&amp;logoColor=white&amp;color=black" /></a>
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<p><a href="https://discord.gg/pYkNyq2TjE"><img alt="Discord" src="https://img.shields.io/discord/1265129134397587457?style=for-the-badge&amp;logo=discord&amp;label=Discord&amp;labelColor=white&amp;color=black" /></a></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="https://omoolab.github.io/BioxelNodes/latest/assets/cover.png" /></p>
<ul>
<li>Realistic 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>Read the <a href="https://docs.omoolab.xyz/bioxelnodes/latest/en/installation">getting started</a> to begin your journey into visualizing volumetric data!</strong></p>
<p>Welcome to our <a href="https://discord.gg/pYkNyq2TjE">discord server</a>, if you have any problems with this add-on.</p>
<h2 id="support-multiple-formats">Support Multiple Formats</h2>
<table>
<thead>
<tr>
<th>Format</th>
<th>EXT</th>
</tr>
</thead>
<tbody>
<tr>
<td>DICOM</td>
<td>.dcm, .DCM, .DICOM, .ima, .IMA</td>
</tr>
<tr>
<td>BMP</td>
<td>.bmp, .BMP</td>
</tr>
<tr>
<td>JPEG</td>
<td>.jpg, .JPG, .jpeg, .JPEG</td>
</tr>
<tr>
<td>PNG</td>
<td>.png, .PNG</td>
</tr>
<tr>
<td>TIFF</td>
<td>.tif, .TIF, .tiff, .TIFF</td>
</tr>
<tr>
<td>Nifti</td>
<td>.nia, .nii, .nii.gz, .hdr, .img, .img.gz</td>
</tr>
<tr>
<td>Nrrd</td>
<td>.nrrd, .nhdr</td>
</tr>
<tr>
<td>HDF5</td>
<td>.hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5</td>
</tr>
<tr>
<td>OME</td>
<td>.ome.tiff, .ome.tif</td>
</tr>
<tr>
<td>MRC</td>
<td>.mrc, .mrc.gz, .map, .map.gz</td>
</tr>
</tbody>
</table>
<h2 id="support-4d-volumetric-data">Support 4D volumetric data</h2>
<p><img alt="4d" src="https://omoolab.github.io/BioxelNodes/latest/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="https://omoolab.github.io/BioxelNodes/latest/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>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="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>
</article>
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<h1 id="improve-performance">Improve Performance</h1>
<p>Voxel reconstruction and voxel rendering are very computation-intensive. Here are some tips to improve the add-on's performance.</p>
<h2 id="use-low-resolution-data-as-preview">Use Low-Resolution Data as Preview</h2>
<p>The resolution of voxels geometrically affects computational efficiency. Enabling Resample on O Layer can greatly improve calculation speed. You can uncheck it when you need to render for real. The Layer Nodes panel in the Bioxel Nodes tab lists all O Layers added in the current geometry nodes. You can uniformly manage whether Resample is enabled and the degree of resampling.</p>
<h2 id="balanced-rendering-settings">Balanced Rendering Settings</h2>
<p>I list some settings that have the greatest impact on volume rendering, so you can find the most suitable balance for your needs.</p>
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<li>
<p><strong>Light Paths &gt; Max Bounces &gt; Volume</strong> affects the number of bounces for volume data. The higher the value, the more transparent the volume data appears.</p>
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<p><strong>Light Paths &gt; Max Bounces &gt; Transparent</strong> affects the number of times transparent surfaces are transmitted. The higher the value, the more transparent the transparent surfaces appear.</p>
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<p><strong>Volumes &gt; Step Rate Render | Viewport</strong> affects the step size of volume rendering. The smaller the value, the more detailed the volume data appears.</p>
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<p>Bioxel Nodes provides some render setting presets for quick configuration. Click the top menu <strong>Bioxel Nodes &gt; Render Setting Presets</strong>, including Performance (left), Balance (center), and Quality (right). Here is a comparison:</p>
<p><img alt="alt text" src="../../assets/render-performance.png" /></p>
<h2 id="rendering-with-eevee">Rendering with EEVEE</h2>
<p>EEVEE doesn't render volume as well as Cycles, but it does have the advantage of rendering volumetric data. If you want to get a clear slice view, it is even a better choice. EEVEE's real-time rendering makes it possible to create interactive content in Blender.</p>
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<h1 id="_1">常见问题</h1>
<h2 id="_2">渲染时场景什么都没有?</h2>
<p>如果您使用 GPU 进行 Cycles 渲染,请确保您的 GPU 支持"Optix",因为 Bioxel Nodes 依赖 OSL(Open Shader Language)进行体渲染,否则您必须使用 CPU 进行渲染。</p>
<p>如果您使用 EEVEE 渲染器,此问题是因为 EEVEE 出于未知原因未加载着色器,保存文件并重启 Blender 即可修复。</p>
<h2 id="_3">更新插件后,文件中的节点变红了?</h2>
<p>这是因为文件中节点的版本与更新后插件的版本不匹配。</p>
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<p>如果您只想让文件正常工作,不再依赖 Bioxel Nodes,那么您只需点击顶部菜单 <strong>Bioxel Nodes &gt; Relink Node Library &gt;</strong>,然后选择相应的版本。检查节点是否正常工作并正确渲染,一切正常后,点击 <strong>Bioxel Nodes &gt; Save Node Library</strong>,在对话框中选择保存位置。</p>
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支持多种格式
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支持 4D 体数据
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<p><strong>v2.0.X 已发布,仅支持 Blender 5.0+,使用方式和之前截然不同,也无法兼容旧版本文件。使用方式查看 http://docs.omoolab.xyz/bioxelnodes/2.0.x/basics/</strong></p>
<h1 id="bioxel-nodes">Bioxel Nodes</h1>
<p><a href="https://blender.org/"><img alt="For Blender" src="https://img.shields.io/badge/Blender-orange?style=for-the-badge&amp;logo=blender&amp;logoColor=white&amp;color=black" /></a>
<img alt="GitHub License" src="https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&amp;labelColor=black" />
<img alt="GitHub Release" src="https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&amp;labelColor=black" />
<img alt="GitHub Repo stars" src="https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&amp;labelColor=black" /></p>
<p><a href="https://discord.gg/pYkNyq2TjE"><img alt="Discord" src="https://img.shields.io/discord/1265129134397587457?style=for-the-badge&amp;logo=discord&amp;label=Discord&amp;labelColor=white&amp;color=black" /></a></p>
<p>Bioxel Nodes 是一款用于科学体数据可视化的 Blender 插件。它利用 Blender 强大的 <strong>几何节点 (Geometry Nodes)</strong> 和 <strong>Cycles</strong> 渲染器来处理和渲染体数据。</p>
<p><img alt="cover" src="https://omoolab.github.io/BioxelNodes/latest/assets/cover.png" /></p>
<ul>
<li>逼真的渲染效果,同时也支持 EEVEE NEXT</li>
<li>支持多种数据格式</li>
<li>支持 4D 体数据</li>
<li>多种切割工具</li>
<li>简洁而强大的节点系统</li>
<li>基于 Blender 原生开发,插件卸载后仍可正常工作</li>
</ul>
<p><strong>阅读<a href="installation/">安装指南</a>开始您的体数据可视化之旅!</strong></p>
<p>如果您在使用过程中遇到任何问题,欢迎加入我们的 <a href="https://discord.gg/pYkNyq2TjE">Discord 服务器</a>。</p>
<h2 id="_1">支持多种格式</h2>
<table>
<thead>
<tr>
<th>格式</th>
<th>扩展名</th>
</tr>
</thead>
<tbody>
<tr>
<td>DICOM</td>
<td>.dcm, .DCM, .DICOM, .ima, .IMA</td>
</tr>
<tr>
<td>BMP</td>
<td>.bmp, .BMP</td>
</tr>
<tr>
<td>JPEG</td>
<td>.jpg, .JPG, .jpeg, .JPEG</td>
</tr>
<tr>
<td>PNG</td>
<td>.png, .PNG</td>
</tr>
<tr>
<td>TIFF</td>
<td>.tif, .TIF, .tiff, .TIFF</td>
</tr>
<tr>
<td>Nifti</td>
<td>.nia, .nii, .nii.gz, .hdr, .img, .img.gz</td>
</tr>
<tr>
<td>Nrrd</td>
<td>.nrrd, .nhdr</td>
</tr>
<tr>
<td>HDF5</td>
<td>.hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5</td>
</tr>
<tr>
<td>OME</td>
<td>.ome.tiff, .ome.tif</td>
</tr>
<tr>
<td>MRC</td>
<td>.mrc, .mrc.gz, .map, .map.gz</td>
</tr>
</tbody>
</table>
<h2 id="4d">支持 4D 体数据</h2>
<p><img alt="4d" src="https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif" /></p>
<p>4D 体数据也可以导入到 Blender 中。</p>
<h2 id="eevee-next">支持 EEVEE NEXT</h2>
<p><img alt="eevee" src="https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif" /></p>
<p>EEVEE NEXT 太棒了!Bioxel Nodes 现在全面支持 EEVEE NEXT!但仍有以下限制:</p>
<ol>
<li>仅支持一个切割器</li>
<li>EEVEE 渲染效果不如 Cycles</li>
</ol>
<h2 id="_2">已知限制</h2>
<ul>
<li>仅支持 Cycles CPU、Cycles GPU (OptiX)、EEVEE</li>
<li>转换为网格时无法生成剖面(即将支持)</li>
</ul>
<h2 id="_3">路线图</h2>
<ul>
<li>更完善的多格式导入体验</li>
<li>一键烘焙带纹理模型</li>
<li>AI 分割生成标签</li>
</ul>
</article>
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<h1 id="_1">安装</h1>
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<h1 id="_1">提升性能</h1>
<p>体素重建和体素渲染是非常消耗计算资源的,以下是一些提升插件性能的建议。</p>
<h2 id="_2">使用低分辨率数据作为预览</h2>
<p>体素的分辨率几何倍地影响计算效率,O Layer 的 Resample 开启可以大大提高计算速度。当你需要正式渲染的时候再关闭即可。在 Bioxel Nodes 分页的 Layer Nodes 面板罗列了当前几何节点中添加的所有 O Layer,你可以统一管理是否开启 Resample,以及程度。</p>
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<p><strong>Light Paths &gt; Max Bounces &gt; Volume</strong> 影响体数据的反弹次数,值越高,体数据看起来越透明。</p>
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<p>Bioxel Nodes 提供了一些渲染设置预设以便快速配置。点击顶部菜单 <strong>Bioxel Nodes &gt; Render Setting Presets</strong>,包括 Performance(左侧)、Balance(中间)和 Quality(右侧)。以下是它们的比较。</p>
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<h2 id="eevee">使用 EEVEE 渲染</h2>
<p>EEVEE 渲染体数据不如 Cycles,但它确实有渲染体数据的优势,如果您想获得清晰的切片视图,它甚至是更好的选择。EEVEE 的实时渲染使得在 Blender 中创建交互式内容成为可能。</p>
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