1010 lines
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HTML
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1010 lines
37 KiB
HTML
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<meta name="description" content="Bioxel Nodes is a Blender add-on for scientific volumetric data visualization.">
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Bioxel Nodes Docs
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高级用法
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中文
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<a href="../en/advanced_usage/" hreflang="en" class="md-select__link">
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English
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正在初始化搜索引擎
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</div>
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<div class="md-header__source">
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<a href="https://github.com/OmooLab/BioxelNodes" title="前往仓库" class="md-source" data-md-component="source">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.6.0 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>
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OmooLab/BioxelNodes
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<li class="md-tabs__item">
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<a href=".." class="md-tabs__link">
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Bioxel Nodes
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</a>
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<a href="../installation/" class="md-tabs__link">
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快速开始
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</a>
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<li class="md-tabs__item">
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<a href="../SARS-Cov-2/" class="md-tabs__link">
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案例教程
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</a>
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Bioxel Nodes Docs
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.6.0 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>
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<div class="md-source__repository">
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OmooLab/BioxelNodes
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Bioxel Nodes
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<h1 id="_1">高级用法</h1>
|
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<h2 id="_2">概念</h2>
|
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<p>在上一节中,我提到了一些关键概念,这里我将详细描述它们,以便您更好地理解后续操作。</p>
|
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<h3 id="_3">容器</h3>
|
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<p>首先是 <strong>容器 (Container)</strong>,它最容易描述,您可以将其想象为一个场景,或一个求解器容器。它是承载所有内容的舞台。</p>
|
||
<h3 id="_4">图层</h3>
|
||
<p>其次是 <strong>图层 (Layer)</strong>,它表示同一容器中同一对象在不同位置的不同数据字段。就像任何地图应用中的视图图层,一个显示道路,一个显示卫星图,而在 Bioxel 中,一个显示 MRI,一个显示 CT,一个显示电信号等。有些图层用于材质,如颜色、密度等,我们称它们为 <strong>材质图层 (Material Layer)</strong>。一个容器包含同一对象的不同图层。任何导入容器的外部数据都会转换为图层。</p>
|
||
<h3 id="_5">组件</h3>
|
||
<p>最后是 <strong>组件 (Component)</strong>,它是 <strong>材质图层</strong> 的一个片段。同一区域中可能存在多个具有不同呈现意义的材质(物质),就像 Blender 中的对象,每个代表场景的一部分。Bioxel Nodes 提供了一系列节点和工具,允许用户基于其他图层(作为源数据)创建材质图层(组件)。在上一节中,我们使用 CT 数据(图层)来制作颅骨的材质(物质),这个过程称为<strong>材质化 (materialization)</strong>。</p>
|
||
<h2 id="_6">将肌肉附着到颅骨</h2>
|
||
<p>一个容器中可以存在多个组件,就像一个场景中可以存在多个对象一样。它们可以单独控制,也可以相互组合以构建复杂的场景。接下来,让我们从 VHP 解剖图像中提取肌肉,并将其附着到上一节创建的颅骨上。解剖图像非常大,为了便于使用,我将其裁剪并缩放到原始大小的 1/4。下载文件并解压到新文件夹。</p>
|
||
<p><a href="https://drive.google.com/file/d/164AjQX0tmgUpWZlleJ5i1IKHco4ytDu2/view?usp=drive_link">VHP_M_AnatomicalImages_Head.zip</a></p>
|
||
<p>您也可以直接从官方网站下载数据:<a href="https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html">https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html</a></p>
|
||
<p>首先按<a href="../step_by_step/">分步指南</a>中所述导入 CT 数据。然后导入解剖图像,但与之前不同的是,这次从现有容器的几何节点菜单(不是顶部菜单)中点击 <strong>Bioxel Nodes > Import Volumetric Data (Init) > as Color</strong>,定位到解压后的文件夹,选择任意一个 .png 文件(不要多选,也不要选择文件夹)。这样导入的图层将与之前的 CT 数据位于同一容器中。您也可以通过将其拖入容器几何节点界面而不是 3D 视图界面来导入。另外请注意,点击的是 <strong>as Color</strong>(而不是 as Scalar),因为解剖图像是 RGB 数据。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image.png" /></p>
|
||
<p>这次让我们在导入选项上多花点时间。首先谈谈选项中的 <strong>Original Spacing</strong> 是什么,您可以简单地将其理解为图像的原始"像素大小"。由于体数据是 3D 的,其像素(即体素)是长方体而不是 2D 矩形,它们有长度、宽度和高度,这就是 <strong>Spacing</strong>。</p>
|
||
<p>通常,Bioxel Nodes 可以从数据头文件中读取间距,您不需要填写该值,但任何 PNG 图像都没有记录该信息,因此您需要手动输入。在 VHP 的官方说明中,解剖图像的每个像素对应 0.33mm 的大小,每个切片的厚度为 1mm,因此解剖图像的 Original Spacing 应设置为 <code>(0.33, 0.33, 1)</code>。</p>
|
||
<p>但是,我提供的文件已将每个图像缩放了 1/4,因此 X 和 Y 轴需要乘以 4。所以最终的 Original Spacing 应设置为 <code>(1.33, 1.33, 1)</code>,这应该很容易理解,对吧?(如果您导入的是官方文件,则仍应设置为 <code>(0.33, 0.33, 1)</code>)
|
||
Layer Name 应设置为 "Anatomical Images",其他选项保持默认,点击确定。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-1.png" /></p>
|
||
<p>导入完成后,在新创建的 "Fetch Layer" 节点之后连接 "Cutout by Hue" 节点(Add > Bioxel Nodes > Component > Cutout by Hue),并打开 Slice Viewer 模式预览,如下图所示。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-2.png" /></p>
|
||
<p>除了间距,Dicom 文件还记录了对象的位置和方向,但这些信息显然没有记录在 PNG 格式中。这导致 CT 数据和解剖图像在位置上不匹配。我们需要手动对齐这两个图层:首先,将 "Cutout by Threshold" 节点的阈值设置为 0.2,以便可以提取并显示完整的头部。然后在 "Cutout by Hue" 节点和 "Cutout by Threshold" 节点之前各添加一个 "ReCenter" 节点,然后在"解剖图像"工作流程中添加 Locater(详见<a href="../step_by_step/">分步指南</a>),最后添加 "Join Component" 节点(Add > Bioxel Nodes > Component > Join Component),并按如下图所示连接和设置参数。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-3.png" /></p>
|
||
<p>"Join Component" 节点允许您将两个组件合并在一起。移动和旋转 Locater 对象,使两个组件的位置完全一致。如果您难以对齐,以下是 Locater 对象属性的精确变换值。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-4.png" /></p>
|
||
<p>接下来让我们分别提取肌肉。</p>
|
||
<p>首先谈谈 "Cutout by Hue" 节点。它的名称表明通过颜色色调提取区域。如果您选择此节点并按 "M" 键暂时静音它,您会看到数据在 Slice Viewer 模式下变成一个带有蓝色部分的立方体。"Cutout by Hue" 节点的默认 Hue 值是红色,这意味着该节点保留接近红色的区域,并去除蓝色(它在色调环上与红色相对),留下人体部分。</p>
|
||
<p>如果调低 Sensitivity 的值,您会看到可见部分减少,只留下更接近红色的部分,而肌肉恰好是红色的,因此我们可以轻松提取肌肉。标本组织的颜色不如活体状态那样鲜艳,我们可以使用 "Set Color by Color" 节点(Add > Bioxel Nodes > Property > Set Color by Color)来微调颜色以恢复活力。</p>
|
||
<p>最后,按如下图所示连接和设置节点,其中 "Set Color by Ramp 2" 节点中的两个颜色是 <code>E7D2C5</code> 和 <code>FFEDEC</code>。如果一切正常,您将获得如下图所示的渲染结果。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-5.png" /></p>
|
||
<p>您还可以在末尾和所有组件上添加 "Transform" 和 "Cutter" 节点。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-6.png" /></p>
|
||
<p>VHP 的多模态数据没有任何变形或缩放差异,只有位置差异,因此所有数据都可以轻松对齐。然而,在大多数情况下,不同模态之间的差异非常大,需要先进行配准,目前 Bioxel Nodes 尚不支持(但在计划中)。尽管如此,您可以基于同一图层构建不同的组件并将它们组合在一起。例如,基于 CT 数据,使用 "Cutout by Range" 节点可以消除低值区域(脂肪),消除高值区域(骨骼),仍能得到肌肉。然后将其附着到颅骨上。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-7.png" /></p>
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<p>然而,大脑和肌肉的 CT 值非常接近,因此通过阈值将大脑与肌肉分离极其困难。那么应该如何提取大脑呢?</p>
|
||
<h2 id="_7">提取大脑</h2>
|
||
<p>我们可以使用 AI 技术来实现大脑区域的划分,这个过程称为<strong>分割 (Segmentation)</strong>,大脑区域称为<strong>标签 (Label)</strong>。医学图像分割有很多模型和方法,这里推荐 <a href="https://github.com/wasserth/TotalSegmentator">Total Segmentator</a>。</p>
|
||
<p>这是一个开箱即用的 CT/MRI 医学图像分割 Python 库。您可以在本地部署 Total Segmentator,也可以通过官方在线网站 <a href="https://totalsegmentator.com">https://totalsegmentator.com</a> 处理您的数据。</p>
|
||
<p>让我演示一下操作,我们仍然使用 VHP 的 CT 数据。点击 "Drop DICOM.zip or..." 并选择 VHP_M_CT_Head.zip 文件。在 "Selected task" 下方输入 "brain",按 Enter 确认。最后点击 "Process data" 按钮。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-8.png" /></p>
|
||
<p>等待上传和处理,之后您将被重定向到以下页面,点击 "Download results" 按钮,下载并解压 segmentations.zip 到任意文件夹。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-9.png" /></p>
|
||
<p>如果您无法获取大脑分割(标签),可以直接下载(无需解压)。</p>
|
||
<p><a href="https://drive.google.com/file/d/1KGiZ3G11YLXkGszSrvWQ9kTF4TMpxUPd/view?usp=drive_link">VHP_M_CT_Head_Brain.nii.gz</a></p>
|
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<p>接下来,我们以与导入解剖图像相同的方式将大脑分割(标签)导入到容器中(在同一容器下),但这次选择 <strong>as Label</strong>,Layer Name 设置为 "Brain",其他选项保持默认。导入完成后,会添加一个新的 "Fetch Layer" 节点。按如下图所示创建和设置节点,您应该能够看到大脑表面。</p>
|
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<p><img alt="alt text" src="../assets/advanced_usage/image-10.png" /></p>
|
||
<p>您看到表面上有"台阶"状的形状了吗?这是因为 AI 分割结果精度较低。那么如何解决这个问题?选择大脑标签的 Fetch Layer 节点,右键弹出菜单,点击 <strong>Bioxel Nodes > Resample Value</strong>,在对话框中,将 "Smooth Size" 更改为 3 或更高(数值越高,计算越慢),点击确定并等待计算完成。完成后,会添加一个新的图层,替换原来的图层,它更平滑了吗?下图列出了不同平滑级别的效果。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-11.png" /></p>
|
||
<p>越平滑,看起来越舒服,但这也意味着丢失更多细节,计算也更慢。</p>
|
||
<p>但是,如果您切开大脑,会发现截面是均匀的,这是因为标签类型图层本身不包含任何模态数据。Bioxel Nodes 提供了一种通过标签填充任意图层值的功能,如果您将 CT 数据中非大脑区域的脑组织值设置得低于大脑组织的 Hu 值,那么任何 "Cutout" 节点将只保留大脑区域。</p>
|
||
<p>操作如下:选择 CT 数据的 "Fetch Layer" 节点,右键弹出菜单,点击 <strong>Bioxel Nodes > Fill Value by Label</strong>,在对话框中,Label 设置为新导入的大脑标签图层,Fill Value 设置为 -100(只要小于大脑组织的 Hu 值即可),点击确定。等待数据处理,完成后会向容器添加一个新的数据图层。</p>
|
||
<p>如下图所示,连接节点并设置节点参数,其中 "Set Color by Ramp 2" 节点的两个颜色是 <code>B26267</code> 和 <code>EBC5B7</code>,"Cutout by Range" 和 "Set Color by Ramp 2" 节点改为 "Value" 模式(默认是 "Factor" 模式),因为大脑的最大值和最小值太接近,在 "Factor" 模式下难以调整。为了使脑组织看起来更透明,我在末尾添加了 "Set Properties"(Add > Bioxel Nodes > Property > Set Properties)节点并将 "Density" 改为 0.5。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-12.png" /></p>
|
||
<p>(仍然觉得不够平滑?目前很难完全摆脱"台阶"表面。)</p>
|
||
<p>现在大脑完成了。最后,我们将所有内容组合在一起,您将得到如下图所示的结果。</p>
|
||
<p><img alt="alt text" src="../assets/advanced_usage/image-13.png" /></p>
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<p>如果您按照文档走到了这一步,为自己鼓掌吧,您已经掌握了这个插件!如果您按照文档操作有困难,可以下载项目文件来理解节点的工作方式。</p>
|
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<p><a href="https://drive.google.com/file/d/1EHB7sxNSvJNwmoTfFnpyOSsm2M_2Y0hO/view?usp=drive_link">VHP.zip</a></p>
|
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<p>AI 分割是体数据可视化的重要组成部分。因此,未来的 Bioxel Nodes 将集成一些常用的 AI 分割模型,让用户可以就地完成体数据可视化!</p>
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