这项工作得到了美国国家心理健康研究所奖 R01 MH131586（授予 PL 和 MR）、R01 MH078113（授予 MK）和 Sydney R Baer Jr 基金会资助（授予 PL）的支持。

本协议已获得贝斯以色列女执事医疗中心机构审查委员会的批准。使用脑部 MRI 扫描没有伪影或运动的健康受试者进行该协议演示，并获得书面知情同意书。使用带有 32 通道头线圈的 3.0 T MRI 扫描仪（参见 材料表）采集分辨率为 1 mm x 1 mm x 1.2 mm 的 3D-T1 图像。使用 MP-RAGE ASSET 序列，视场为 256 x 256，TR/TE/TI=7.38/3.06/400 ms，翻转角度为 11 度。
1. 将脑部 MRI 导入 3D 切片器
注意：3D Slicer 提供与其用户界面相关的文档。
<ol><li>准备脑部 MRI DICOM（医学中的数字成像和通信）或 NIFTI（神经影像信息学技术计划）文件以导入到 3D Slicer。</li>
	<li>通过单击工具栏左上角的 DCM 按钮导入 DICOM 数据。然后单击 导入 DICOM 文件 按钮导入 DICOM 格式数据。</li>
	<li>如果 MRI 数据为 NIFTI 格式，请单击工具栏左上角 的 DATA 按钮导入它。在弹出的对话框中，选择 “选择要添加的目录 以批量导入文件夹中的 NIFTI 数据”，或选择“ 选择要添加的文件” 以导入特定的 NIFTI 文件。然后，点击 OK 按钮继续将数据上传到 3D Slicer。</li>
	<li>导入后，MRI 数据将出现在右侧的窗口中，显示轴向、矢状面和日冕平面。</li>
	<li>通过导航到 “布局 ”并选择特定布局来更改窗口的布局。这可以通过单击 3D Slicer 工具栏本身的 Layouts 模块图像或通过应用程序菜单中的 View > Layouts 找到。</li>
</ol>2. 从 3D Slicer 中的示例数据下载 DICOM
<ol><li>单击“欢迎使用切片器”部分打开屏幕中的“下载示例数据”按钮。然后选择 MRHead 按钮，它将开始下载过程，这可能需要几分钟时间。</li>
	<li>确保右侧窗口显示轴向、矢状面和冠状面的脑部 MRI 数据。</li>
</ol>3.质量控制和调整MRI图像
<ol><li>通过严格审查每个 MRI 切片，定性地确定图像质量以及由于头部运动或扫描问题而导致的伪影的存在。</li>
	<li>通过 右键单击并分别向上或向下移动鼠标 来缩小或缩小图像切片。</li>
	<li>若要移动图像切片， 请左键单击 图像，按住 Shift 键，然后拖动鼠标。</li>
	<li>调整图像亮度有助于观察脉络丛。为此，请单击工具栏中的 “调整窗口/音量级别 ”或 左键单击 图像并 向上或向下移动鼠标 以分别提高或降低亮度。</li>
	<li>调整对比度还有助于找到脉络丛。 左键单击 图像切片，然后 向左或向右移动鼠标 以分别增加或减少对比度。要确定脉络丛的适当对比度，请使用深层灰质核（排列在侧脑室和第三脑室周围的灰质中心块）或对比度比例尺中显示的信号强度。</li>
	<li>选择首选对比度后，在整个分割过程中保持相同的对比度，并且不要针对幕上和幕下区域的潜在变化进行调整。</li>
</ol>4. 创建脉络丛的手动节段
<ol><li>要开始分割外侧、第三和第四室脉络丛，请在 “分段编辑器 ”模块中创建分割文件。要导航到那里，请单击工具栏中的 区段编辑器 ，或转到 模块：下拉菜单，然后选择 区段编辑器。</li>
	<li>单击 细分 的下拉菜单以选择不同的细分（如果创建了多个细分）并重命名当前选定的细分。</li>
	<li>使用 “主音量 ”下拉列表选择需要编辑的 NIFTI 或 DICOM 集。只有选择卷文件后，用户才能开始分段/编辑。</li>
	<li>单击 “添加 ”按钮两次，为侧脑室脉络丛添加两个节段。要重命名这些名称，请 双击 名称并将它们更改为 右外侧心室脉络丛 和 左外侧心室脉络丛。</li>
	<li>再次单击“添加”按钮以添加第三和第四室脉络丛的段，并将其重命名为“第三室脉络丛”和“第四室脉络丛”。</li>
</ol>5. 查看不同的切片和分割
<ol><li>在编辑之前，请执行背景研究，以了解如何在查看窗口中的布局之间移动以及如何更改分段的视图或不透明度。</li>
	<li>在查看窗口的顶部和切片滑块的左侧，单击 图钉图标。这将打开一个下拉菜单，该菜单可能因窗口所在的特定布局而异。 注意：在分割脉络丛时，使用不同的布局可能会有所帮助，因为它的结构可能因人而异。例如，“常规”布局允许用户同时查看所有三个切片和场景的 3D 视图。选择“仅红色/黄色/绿色切片”可让用户获得 2D 切片的特写视图，以便更精确地分割脉络丛。</li>
</ol>6. 描绘侧脑室脉络丛 ROI
注意：手动分割不需要将图像注册到模板。
<ol><li>对于 侧脑室脉络丛，从 轴向平面 开始，确保图像基于双线定位。然后使用 三角侧支作为 定位侧脑室脉络丛的参考点。<ol><li>在轴向平面上进行编辑后，移动到其余视图（矢状面和冠状面），以确保侧脑室脉络丛的手动分割不会捕获周围的脑实质或脑脊液。</li>
	</ol></li>
	<li>要开始编辑，请单击要处理 的区段 ，区段名称将突出显示。</li>
	<li>单击“片段编辑器”的“效果”部分中的“绘制”或“绘制”工具，开始手动分割。 注意：最好在一个平面（日冕、轴向或矢状面）开始分割，并在所有切片中完成分割后，移动到其他平面以检查和优化手动分割。建议用户从轴向或冠状平面开始，因为在这些视图中更容易看到侧脑室脉络丛。</li>
	<li>使用 绘制 工具时， 左键单击并按住 以在侧脑室脉络丛边界处绘制轮廓。跟踪后， 右键单击 以填充绘制区域。</li>
	<li>使用 “绘画 ”工具时，首先选择要用于绘画的画笔的直径。建议使用 3% 或 5% 的刷子来更精确地描绘脉络丛，而 10% 可用于更大的选择。</li>
	<li>对于任一工具，请使用 “绘制 ”或 “擦除 ”通过添加或删除选区来纠正任何错误的描绘。 注意：参考其他视图平面可以帮助识别侧脑室脉络丛结构与其他大脑结构，例如周围的灰质、穹窿、胼胝体或海马体。鼓励用户排除已识别脉络丛囊肿的脑部扫描。</li>
	<li>使用红核的水平作为停止侧脑室脉络丛分割的标志。</li>
</ol>7. 描绘第三和第四脑室脉络丛 ROI
注意：更高分辨率的 T1w 图像（例如 0.7 或 0.8 毫米）和在 7T MRI 上获得的图像将提供更准确和可靠的第三和第四脑室脉络丛的手动分割。分割第三和第四脑室脉络丛比侧脑室脉络丛更困难，因为这些区域可能要小得多，并且需要描绘的体素更少。
<ol><li>对于 第三脑室脉络丛，从 矢状面 开始，以 门罗孔、穹窿孔、胼胝体、丘脑和大脑内静脉 为参考点，精确定位第三脑室 脉络丛。在同一平面内的切片之间移动有助于确定一个区域是穹窿、丘脑、静脉还是第三室脉络丛。<ol><li>在矢状面上进行编辑后，导航到其余视图（轴向和冠状），以确保第三室脉络丛的手动分割不会选择周围的脑实质或脑脊液。</li>
	</ol></li>
	<li>同样，对于 第四脑室脉络丛，从 矢状面 开始，使用 小脑上蒂、脑桥和延髓作为参考点 ，以精确定位第四脑室中的脉络丛。在同一平面内的切片之间移动有助于确定一个区域是小脑、小脑扁桃体、髓下腭还是第4 脑室 脉络丛。<ol><li>在矢状面完成编辑后，移动到其余视图（轴向和冠状），以确保第四脑室脉络丛的手动分割不会选择周围的脑实质或脑脊液。</li>
	</ol></li>
</ol>8. 计算脉络丛的体积
<ol><li>从 模块 下拉菜单中，导航到 量化 ，然后选择 细分统计。</li>
	<li>在 输入下，在 分割 工具下选择要量化的新分割图，然后从 标量体积中选择 MRI 体积。对于 输出表 （ 输出）， 选择表选项 。完成后，按 应用，包含脉络丛体积的表格将以各种单位出现。</li>
</ol>9. 保存区段和交易量结果
<ol><li>点击 保存 工具 栏左上角的按钮以保存生成的文件。</li>
	<li>将分割文件另存为 .nrrd （3D 切片器文件）、 .nii.gz （NIFTI 文件）或 .tsv （表文件）。</li>
</ol>10. 确定分段的准确性、性能和一致性
注意：建议使用 MONAI 软件包（参见 材料表），它描述了骰子系数 （DC） 和 DeepMind 平均表面距离 （avgSD）。下面介绍了 DC 和 avgSD 的详细信息。为了计算这些指标，读者需要知道如何编程（例如，python，从磁盘读取图像，将数据重新格式化为这些函数的适当输入数组）。没有包含所有这些指标的用户友好型软件包。
<ol><li>DC 分数是量化两个几何域重叠的标准方法。要计算两个分段之间的平均 DC 分数，请提供两个张量 y_pred 和 y，即多帧图像，每个二值化标签图像一个帧。张量 y_pred 和 y 可能包含两个不同手动评分器的分割、同一评分器的重复分割或自动预测和手动地面实况。<ol><li>使用函数 monai.metrics.compute_meandice 计算平均 DC 分数。</li>
		<li>使用 monai.transforms.post 生成合适的二进制标签张量。 注意：可以将 include_background 参数设置为 False，以从 DC 计算中排除第一类（通道索引 0），按照惯例，该类别被假定为背景。</li>
	</ol></li>
	<li>考虑 avgSD 分数 不太常见，并注意该方法可能会有所不同，因为存在多个表面距离定义。例如，使用最大距离（也称为豪斯多夫距离，对异常值高度敏感）、平均距离（如此处所述）和第 95 个百分位数（高度稳健）作为常用度量。<ol><li>使用函数 compute_average_surface_distance 计算 avgSD 分数。</li>
		<li>确保此函数在默认设置下计算从 y_pred 到 y 的平均表面距离。</li>
		<li>此外，如果 symmetric = True，请确保返回这两个输入之间的平均对称曲面距离。</li>
	</ol></li>
	<li>通过使用强大的 Wilcoxon 符号秩检验进行配对分析，可以对多个案例的 DC 和 avgSD 分数进行统计分析。</li>
	<li>考虑使用班级内相关系数 （ICC） 作为另一种常用方法，以确定不同评分者是否可以对多个参与者进行可靠评分。请记住，ICC 对一组配对的分割测量值（例如体积）进行操作，而不是直接对分割图像进行操作。若要计算 ICC，请使用 R 软件和 R Studio（请参阅 材料表），这使得该过程变得简单明了。<ol><li>使用 install.packages（“psych”） 下载软件包并加载库 （psych）。</li>
		<li>使用 Data <- data.frame（df） 输入数据框，其中包括每列中的参与者（行）和评分者。然后使用绘图（数据）可视化测量结果。</li>
		<li>要运行 ICC，请使用 ICC（Data），它会生成不同类型 ICC 的表，例如，获取评分者之间或内部的分数。</li>
	</ol></li>
</ol>

加强脑部疾病的神经影像学分析

作者没有相互竞争的经济利益。

协议的关键步骤 在实施该协议时，需要特别注意三个关键步骤。首先，检查MR图像的质量和对比度是确保准确分割的关键。如果图像质量太差，或者对比度太低或太高，都可能导致脉络丛的描绘不准确。可以通过查看图像的灰度值或校准值来增强灰质核和灰质之间的对比度来调整图像的对比度。其次，评估者需要熟悉脉络丛的解剖结构并接受过专门培训。如果评估者不熟悉脉络丛?...

脉络丛功能 脉络丛是大脑中高度血管化的结构，由开窗的毛细血管和单层脉络丛上皮细胞组成 1。脉络丛投射到外侧、第三和第四脑室并产生脑脊液 （CSF），脑脊液在神经模式2 和脑生理学 3,4 中起重要作用。脉络丛分泌神经血管物质，包含干细胞样储存库，并作为阻止有毒代谢物进入的物理屏障，去除绕过物理屏障的部分的酶屏障，以及防止外来入侵者的免疫屏障5。脉络丛调节神经发生6、突触可塑性7、炎症8、昼夜节律9、10、肠脑轴11 和认知12。此外，外周细胞因子、应激和感染（包括 SARS-CoV-2）会破坏血液脑脊液屏障13、14、15、16。因此，脉络丛-脑脊液系统是神经发育、神经回路成熟、脑稳态和修复不可或缺的一部分 17。由于免疫、炎症、代谢和酶促改变会影响大脑，研究人员正在使用神经影像学工具来评估脉络丛在整个生命周期和脑部疾病中的作用 18,19,20。然而，用于脉络丛分割的常用自动化工具（如 FreeSurfer）存在局限性，导致脉络丛分割不良。因此，迫切需要脉络丛的地面实况手动分割，可用于开发用于脉络丛分割的精确自动化工具。
脉络丛在神经发育和脑部疾病中的应用 脉络丛在脑部疾病中的作用长期以来一直被忽视，主要是因为它被认为是一个辅助角色，其作用是缓冲大脑并维持适当的盐平衡2,21。然而，脉络丛作为一种与脑部疾病相关的结构而受到关注，例如疼痛综合征22、SARS-CoV-216、23、24、神经发育2 和脑部疾病19，这表明在行为障碍的发展中具有跨诊断作用。在神经发育障碍中，脉络丛囊肿与发育迟缓、注意力缺陷/多动障碍 （ADHD） 或自闭症谱系障碍 （ASD） 的风险增加有关25,26。此外，发现 ASD27 患者的侧脑室脉络丛体积增加。在脑部疾病中，脉络丛异常自 1921 年以来一直在精神障碍中被描述 28,29。先前的研究已经使用 FreeSurfer 分割在精神障碍患者的大样本中确定了脉络丛增大，与他们的一级亲属和对照组相比 19.在精神病临床高危人群的大样本中使用手动分割的脉络丛体积重复了这些发现，发现与健康对照组相比，这些患者的脉络丛体积更大30。越来越多的研究表明脉络丛肿大在复杂区域疼痛综合征22、中风31、多发性硬化症 20,32、阿尔茨海默氏症33,34 和抑郁症35 中，其中一些证明了外周和大脑免疫/炎症活动之间的联系。这些神经影像学研究很有希望;然而，FreeSurfer21 对侧脑室脉络丛分割不良限制了自动脉络丛体积估计的可信度。因此，多发性硬化症20,32、抑郁症35、阿尔茨海默氏症34 和早期精神病36 的研究已经开始手动分割侧脑室脉络丛，但目前没有关于如何做到这一点的指南，也没有关于分割第三和第四脑室脉络丛的指南。
常见的分割工具排除脉络丛 大脑分割管道，如 FreeSurfer37,38,39、FMRIB 软件库 （FSL）40、SLANT41 和 FastSurfer（由合著者 Martin Reuter 开发）42,43，使用基于图谱 （FSL）、基于图谱和表面的 （FreeSurfer） 以及深度学习分割范式（SLANT 和 FastSurfer）准确可靠地分割皮层和皮层下结构。其中一些方法的缺点包括处理速度、对不同扫描仪的有限泛化、场强和体素大小 37,44，以及在标准图集空间中强制对齐标签图。然而，脉络丛分割的能力以及与高分辨率 MRI 的兼容性仅由 FreeSurfer 和 FastSurfer 解决。FastSurfer 背后的神经网络是在 FreeSurfer 脉络丛标签上训练的，因此它们继承了 FreeSurfer 之前讨论的可靠性和覆盖范围限制，第三和第四脑室被忽略21。目前高分辨率 MRI 也存在局限性，但 FreeSurfer 的高分辨率流45 和 FastSurferVINN43 可用于处理此问题。
当前的脉络丛分割工具 脉络丛只有一种免费可用的分割工具，但分割精度有限。准确的脉络丛分割可能受到多种因素的影响，包括 （1） 脉络丛位置的变异性（空间上非平稳的），这是由于其在心室内的位置，（2） 体素强度、对比度、分辨率（结构内异质性）的差异，由于细胞异质性、动态脉络丛功能、病理变化或部分体积效应，（3） 影响脉络丛大小的年龄或病理学相关的心室大小差异， （4）靠近相邻的皮质下结构（海马体、杏仁核、尾状核和小脑），这些结构也很难分割。鉴于这些挑战，FreeSurfer 分割经常低估或高估、错误标记或忽略脉络丛。
最近的三篇出版物解决了使用高斯混合模型 （GMM）46、轴向 MLP47 和基于 U-Net 的深度学习方法48 进行可靠脉络丛分割的差距。每个模型都使用最多 150 名受试者的私有、手动标记数据集进行训练和评估，这些受试者的扫描仪、部位、人口统计学和疾病的多样性有限。虽然这些出版物 46,48,49 比 FreeSurfer 的脉络丛分割取得了显着改进——有时将预测和地面实况的交叉点增加了一倍，但这两种方法都没有 （1） 在高分辨率 MRI 中得到验证，（2） 具有专门的泛化和可靠性分析，（3） 具有大型代表性的训练和测试数据集，（4） 专门解决或分析脉络丛分割挑战，例如部分体积效应，或 （5） 作为即用型工具公开提供。因此，目前脉络丛分割的“金标准”是手动追踪，例如，使用 3D Slicer50 或 ITK-SNAP51，这在以前没有描述过，对于希望检查脉络丛在其研究中的作用的研究人员来说，这是一个重大挑战。之所以选择3D Slicer进行手动分割，是因为作者熟悉该软件，并且因为它为用户提供了基于不同方法的各种工具，这些工具可以组合在一起以获得所需的结果。可以使用其他工具，例如主要面向图像分割的ITK-SNAP，一旦掌握了该工具，用户就可以获得良好的效果。此外，作者还进行了一项病例对照研究，证明了他们使用 3D Slicer30 的手动分割技术的高准确性和可靠性，本文描述了具体方法。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3D Slicer</td>
			<td>3D Slicer</td>
			<td>https://www.slicer.org/</td>
			<td>A free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.</td>
		</tr>
		<tr>
			<td>FreeSurfer</td>
			<td>FreeSurfer</td>
			<td>https://surfer.nmr.mgh.harvard.edu/</td>
			<td>An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images</td>
		</tr>
		<tr>
			<td>ITK-SNAP</td>
			<td>ITK-SNAP</td>
			<td>http://www.itksnap.org/pmwiki/pmwiki.php</td>
			<td>A free, open-source, multi-platform software application used to segment structures in 3D and 4D biomedical images.&#160;</td>
		</tr>
		<tr>
			<td>Monai Package</td>
			<td>Monai Consortium</td>
			<td>https://docs.monai.io/en/stable/metrics.html</td>
			<td>Use for Dice Coefficient and DeepMind average Surface Distance.&#160;</td>
		</tr>
		<tr>
			<td>MRI scanner</td>
			<td>GE</td>
			<td>Discovery MR750&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Psych Package</td>
			<td>R-Project</td>
			<td>https://cran.r-project.org/web/packages/psych/index.html</td>
			<td>A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology.</td>
		</tr>
		<tr>
			<td>R Software</td>
			<td>R-Project</td>
			<td>https://www.r-project.org/</td>
			<td>R is a free software environment for statistical computing and graphics.&#160;</td>
		</tr>
		<tr>
			<td>RStudio</td>
			<td>Posit</td>
			<td>https://posit.co/</td>
			<td>An RStudio integrated development environment (IDE) is a set of tools built to help you be more productive with R and Python.&#160;</td>
		</tr>
		<tr>
			<td>Windows or Apple OS Desktop or Laptop</td>
			<td>Any company</td>
			<td>n/a</td>
			<td>Needed for running the software used in this protocol.&#160;</td>
		</tr>
	</tbody>
</table>

manual segmentation of the human choroid plexus using brain mri

脉络丛与神经发育和一系列脑部疾病有关。有证据表明，脉络丛对大脑成熟、免疫/炎症调节以及行为/认知功能至关重要。然而，目前的自动神经影像学分割工具在准确可靠地分割侧脑室脉络丛方面表现不佳。此外，没有现有的工具可以分割位于大脑第三和第四脑室的脉络丛。因此，需要制定一个方案来描述如何分割侧脑室、第三脑室和第四脑室中的脉络丛，以提高检查神经发育和脑部疾病中脉络丛的研究的可靠性和可复制性。该协议提供了在基于DICOM或NIFTI图像的脉络丛的3D Slicer中创建单独标记文件的详细步骤。脉络丛将使用 T1w 图像的轴向、矢状面和冠状面手动分割，确保从与心室接壤的灰质或白质结构中排除体素。将调整窗口以帮助脉络丛及其解剖边界的定位。评估准确性和可靠性的方法将作为本协议的一部分进行演示。使用手动划定对脉络丛进行金标准分割可用于开发更好、更可靠的自动分割工具，这些工具可以公开共享，以阐明脉络丛在整个生命周期和各种脑部疾病中的变化。

所提出的方法对侧脑室脉络丛进行了迭代改进，涉及对 169 名健康对照和 340 名临床精神病高风险患者的队列进行了广泛测试30。使用上述技术，作者在DC = 0.89，avgHD = 3.27 mm3和单评分者ICC = 0.9730的情况下获得了较高的评分者内部准确性和可靠性，证明了本文所述方案的强度。
处理质量控制问题和 3D 切片器设置 在开始分割过程之前，有?...

Watch this Scientific Journal Video about Bridging Gaps in Anatomy and Establishing a Foundation for Algorithmic Studies at JoVE.com

作者聚焦：弥合解剖学差距并为算法研究奠定基础 

尽管脉络丛在大脑中起着至关重要的作用，但由于缺乏可靠的自动分割工具，这种结构的神经影像学研究很少。本方案旨在确保脉络丛的金标准手动分割，这可以为未来的神经影像学研究提供信息。

使用脑部 MRI 手动分割人脉络丛

The choroid plexus has been implicated in neurodevelopment and a range of brain disorders. Evidence demonstrates that the choroid plexus is critical for ...

我们的目标是建立一个可访问的标准化协议，用于手动分割大脑外侧第三和第四脑室内的脉络丛。我们希望解决手动分割脉络丛时可能出现的任何常见问题或问题，特别是考虑到其在大脑中位置的复杂性。开发该协议将导致创建一个足够大的数据集，该数据集由地面实况分割图组成，然后我们可以使用它来训练和开发能够准确自动分割脉络丛的算法。将来，这将导致研究脉络丛在各种神经和神经精神疾病中的作用。

manual-segmentation-of-the-human-choroid-plexus-using-brain-mri

Research

JoVE Journal

Neuroscience

Manual Segmentation of the Human Choroid Plexus Using Brain MRI

2.0K 次观看.  Beth Israel Deaconess Medical Center. 我们的目标是建立一个可访问的标准化协议，用于手动分割大脑外侧第三和第四脑室内的脉络丛。我们希望解决手动分割脉络丛时可能出现的任何常见问题或问题，特别是考虑到其在大脑中位置的复杂性。开发该协议将导致创建一个足够大的数据集，该数据集由地面实况分割图组成，然后我们可以使用它来训练和开发能够准确自动分割脉络丛的算法。将来，这将导致研?...

视频: 作者聚焦：弥合解剖学差距并为算法研究奠定基础 

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains technically challenging. One approach, Activation-Induced Manganese-enhanced MRI (AIM MRI), has been used successfully to map neuronal activity in rodents 1-5. In AIM MRI, Mn2+ acts a calcium analog and accumulates in depolarized neurons 6,7. Because Mn2+ shortens the T1 tissue property, regions of elevated neuronal activity will enhance in MRI. Furthermore, Mn2+ clears slowly from the activated regions; therefore, stimulation can be performed outside the magnet prior to imaging, enabling greater experimental flexibility. However, because Mn2+ does not readily cross the blood-brain barrier (BBB), the need to open the BBB has limited the use of AIM MRI, especially in mice.
One tool for opening the BBB is ultrasound. Though potentially damaging, if ultrasound is administered in combination with gas-filled microbubbles (i.e., ultrasound contrast agents), the acoustic pressure required for BBB opening is considerably lower. This combination of ultrasound and microbubbles can be used to reliably open the BBB without causing tissue damage 8-11.
Here, a method is presented for performing AIM MRI by using microbubbles and ultrasound to open the BBB. After an intravenous injection of perflutren microbubbles, an unfocused pulsed ultrasound beam is applied to the shaved mouse head for 3 minutes. For simplicity, we refer to this technique of BBB Opening with Microbubbles and UltraSound as BOMUS 12. Using BOMUS to open the BBB throughout both cerebral hemispheres, manganese is administered to the whole mouse brain. After experimental stimulation of the lightly sedated mice, AIM MRI is used to map the neuronal response.
To demonstrate this approach, herein BOMUS and AIM MRI are used to map unilateral mechanical stimulation of the vibrissae in lightly sedated mice 13. Because BOMUS can open the BBB throughout both hemispheres, the unstimulated side of the brain is used to control for nonspecific background stimulation. The resultant 3D activation map agrees well with published representations of the vibrissae regions of the barrel field cortex 14. The ultrasonic opening of the BBB is fast, noninvasive, and reversible; and thus this approach is suitable for high-throughput and/or longitudinal studies in awake mice.

A technique is described for broadly opening the blood-brain barrier in the mouse using microbubbles and ultrasound. Using this technique, manganese can be administered to the mouse brain. Because manganese is an MRI contrast agent that accumulates in depolarized neurons, this approach enables imaging of neuronal activity.

使用超声波血脑屏障破坏和锰增强MRI的脑功能成像

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains ...

科研

神经科学

Manual Drainage of the Zebrafish Embryonic Brain Ventricles

Cerebrospinal fluid (CSF) is a protein rich fluid contained within the brain ventricles. It is present during early vertebrate embryonic development and persists throughout life. Adult CSF is thought to cushion the brain, remove waste, and carry secreted molecules1,2. In the adult and older embryo, the majority of CSF is made by the choroid plexus, a series of highly vascularized secretory regions located adjacent to the brain ventricles3-5. In zebrafish, the choroid plexus is fully formed at 144 hours post fertilization (hpf)6. Prior to this, in both zebrafish and other vertebrate embryos including mouse, a significant amount of embryonic CSF (eCSF) is present . These data and studies in chick suggest that the neuroepithelium is secretory early in development and may be the major source of eCSF prior to choroid plexus development7.
eCSF contains about three times more protein than adult CSF, suggesting that it may have an important role during development8,9. Studies in chick and mouse demonstrate that secreted factors in the eCSF, fluid pressure, or a combination of these, are important for neurogenesis, gene expression, cell proliferation, and cell survival in the neuroepithelium10-20. Proteomic analyses of human, rat, mouse, and chick eCSF have identified many proteins that may be necessary for CSF function. These include extracellular matrix components, apolipoproteins, osmotic pressure regulating proteins, and proteins involved in cell death and proliferation21-24. However, the complex functions of the eCSF are largely unknown.
We have developed a method for removing eCSF from zebrafish brain ventricles, thus allowing for identification of eCSF components and for analysis of the eCSF requirement during development. Although more eCSF can be collected from other vertebrate systems with larger embryos, eCSF can be collected from the earliest stages of zebrafish development, and under genetic or environmental conditions that lead to abnormal brain ventricle volume or morphology. Removal and collection of eCSF allows for mass spectrometric analysis, investigation of eCSF function, and reintroduction of select factors into the ventricles to assay their function. Thus the accessibility of the early zebrafish embryo allows for detailed analysis of eCSF function during development.

We present a method to collect cerebrospinal fluid (CSF) and to create a system which lacks CSF within the embryonic zebrafish brain ventricular system. This allows for further examination of CSF composition and its requirement during embryonic brain development.

手动排水的斑马鱼胚胎脑室

Cerebrospinal fluid  (CSF) is a protein rich fluid contained within the brain ventricles. It is  present during early vertebrate embryonic development and ...

A Visual Description of the Dissection of the Cerebral Surface Vasculature and Associated Meninges and the Choroid Plexus from Rat Brain

This video presentation was created to show a method of harvesting the two most important highly vascular structures, not residing within the brain proper, that support forebrain function. They are the cerebral surface (superficial) vasculature along with associated meninges (MAV) and the choroid plexus which are necessary for cerebral blood flow and cerebrospinal fluid (CSF) homeostasis. The tissue harvested is suitable for biochemical and physiological analysis, and the MAV has been shown to be sensitive to damage produced by amphetamine and hyperthermia 1,2. As well, the major and minor cerebral vasculatures harvested in MAV are of potentially high interest when investigating concussive types of head trauma. The MAV dissected in this presentation consists of the pial and some of the arachnoid membrane (less dura) of the meninges and the major and minor cerebral surface vasculature. The choroid plexus dissected is the structure that resides in the lateral ventricles as described by Oldfield and McKinley3,4,5,6. The methods used for harvesting these two tissues also facilitate the harvesting of regional cortical tissue devoid of meninges and larger cerebral surface vasculature, and is compatible with harvesting other brain tissues such as striatum, hypothalamus, hippocampus, etc. The dissection of the two tissues takes from 5 to 10 min total. The gene expression levels for the dissected MAV and choroid plexus, as shown and described in this presentation can be found at GSE23093 (MAV) and GSE29733 (choroid plexus) at the NCBI GEO repository. This data has been, and is being, used to help further understand the functioning of the MAV and choroid plexus and how neurotoxic events such as severe hyperthermia and AMPH adversely affect their function.

This video presentation shows a method of harvesting the two most important highly vascular structures that support forebrain function. They are the cerebral surface (superficial) vasculature along with associated meninges (MAV) and the choroid plexus which are necessary for cerebral blood flow and cerebrospinal fluid (CSF) homeostasis.

从大鼠脑的解剖脑表面血管及相关脑膜和脉络丛的可视描述，

This video presentation was created to show a method of harvesting the two most important highly vascular structures, not residing within the brain ...

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, hippocampus, and the associated parahippocampal regions (perirhinal, entorhinal,&#160;and parahippocampal proper). Unlike most other tracing protocols available, typically focusing on certain MTL areas (e.g., amygdala and/or hippocampus), the integrative perspective adopted by the present tracing guidelines allows for clear localization of all MTL subregions. By integrating information from a variety of sources, including extant tracing protocols separately targeting various MTL structures, histological reports, and brain atlases, and with the complement of illustrative visual materials, the present protocol provides an accurate, intuitive, and convenient guide for understanding the MTL anatomy. The need for such tracing guidelines is also emphasized by illustrating possible differences between automatic and manual segmentation protocols. This knowledge can be applied toward research involving not only structural MRI investigations but also structural-functional colocalization and fMRI signal extraction from anatomically defined ROIs, in healthy and clinical groups alike.

The present work provides a comprehensive set of guidelines for manually tracing the medial temporal lobe (MTL) structures. This protocol can be applied to research involving structural and/or combined structural-functional magnetic resonance imaging (MRI) investigations of the MTL, in both healthy and clinical groups.

一个全面协议的内侧颞叶结构的手动分割

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, ...

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (&#62;3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice&#39;s kappa metric. Mean Dice&#39;s kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

高分辨率<em&gt;在体内</em&gt;使用3T磁共振成像手动分割协议为人类海马子字段

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has ...

Observation of the Ciliary Movement of Choroid Plexus Epithelial Cells Ex Vivo

The choroid plexus is located in the ventricular wall of the brain, the main function of which is believed to be production of cerebrospinal fluid. Choroid plexus epithelial cells (CPECs) covering the surface of choroid plexus tissue harbor multiple unique cilia, but most of the functions of these cilia remain to be investigated. To uncover the function of CPEC cilia with particular reference to their motility, an ex vivo observation system was developed to monitor ciliary motility during embryonic, perinatal and postnatal periods. The choroid plexus was dissected out of the brain ventricle and observed under a video-enhanced contrast microscope equipped with differential interference contrast optics. Under this condition, a simple and quantitative method was developed to analyze the motile profiles of CPEC cilia for several hours ex vivo. Next, the morphological changes of cilia during development were observed by scanning electron microscopy to elucidate the relationship between the morphological maturity of cilia and motility. Interestingly, this method could delineate changes in the number and length of cilia, which peaked at postnatal day (P) 2, while the beating frequency reached a maximum at P10, followed by abrupt cessation at P14. These techniques will enable elucidation of the functions of cilia in various tissues. While related techniques have been published in a previous report1, the current study focuses on detailed techniques to observe the motility and morphology of CPEC cilia ex vivo.

Observation of the Ciliary Movement of Choroid Plexus Epithelial Cells Ex Vivo

In this study, a detailed light microscopic technique was optimized for real-time observation and analysis of the motion of CPEC cilia ex vivo together with an electron microscopic method for ultrastructural analysis.

脉络丛上皮细胞的纤毛运动的观察<em&gt;离体</em

The choroid plexus is located in the ventricular wall of the brain, the main function of which is believed to be production of cerebrospinal fluid. ...

Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images

Within neuroimaging research, a number of recent studies have discussed the impact of between-study differences in volumetric findings that are thought to result from the use of different segmentation tools to generate brain volumes. Here, processing pipelines for seven automated tools that can be used to segment grey matter within the brain are presented. The protocol provides an initial step for researchers aiming to find the most accurate method for generating grey matter volumes from T1-weighted MRI scans. Steps to undertake detailed visual quality control are also included in the manuscript. This protocol covers a range of potential segmentation tools and encourages users to compare the performance of these tools within a subset of their data before selecting one to apply to a full cohort. Furthermore, the protocol may be further generalized to the segmentation of other brain regions.

This protocol describes the process of applying seven different automated segmentation tools to structural T1-weighted MRI scans to delineate grey matter regions that can be used for the quantification of grey matter volume.

t1 加权 mri 图像中皮质灰质的自动分割

Within neuroimaging research, a number of recent studies have discussed the impact of between-study differences in volumetric findings that are thought to ...

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of structural changes caused by genetic or environmental perturbations. Whole-brain imaging results in more accurate quantification of cells and the study of region-specific differences that may be missed with commonly used microscopy of physically sectioned tissue. Using light-sheet microscopy to image cleared brains greatly increases acquisition speed as compared to confocal microscopy. Although these images produce very large amounts of brain structural data, most computational tools that perform feature quantification in images of cleared tissue are limited to counting sparse cell populations, rather than all nuclei.
Here, we demonstrate NuMorph (Nuclear-Based Morphometry), a group of analysis tools, to quantify all nuclei and nuclear markers within annotated regions of a postnatal day 4 (P4) mouse brain after clearing and imaging on a light-sheet microscope. We describe magnetic resonance imaging (MRI) to measure brain volume prior to shrinkage caused by tissue clearing dehydration steps, tissue clearing using the iDISCO+ method, including immunolabeling, followed by light-sheet microscopy using a commercially available platform to image mouse brains at cellular resolution. We then demonstrate this image analysis pipeline using NuMorph, which is used to correct intensity differences, stitch image tiles, align multiple channels, count nuclei, and annotate brain regions through registration to publicly available atlases.
We designed this approach using publicly available protocols and software, allowing any researcher with the necessary microscope and computational resources to perform these techniques. These tissue clearing, imaging, and computational tools allow measurement and quantification of the three-dimensional (3D) organization of cell-types in the cortex and should be widely applicable to any wild-type/knockout mouse study design.

This protocol describes methods for conducting magnetic resonance imaging, clearing, and immunolabeling of intact mouse brains using iDISCO+, followed by a detailed description of imaging using light-sheet microscopy, and downstream analyses using NuMorph.

使用MRI，组织清除和光片显微镜对完整的新生小鼠大脑进行全脑单细胞成像和分析

Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of ...

Microdissection and Whole Mount Scanning Electron Microscopy Visualization of Mouse Choroid Plexus

The choroid plexus (CP), a highly vascularized structure protruding into the ventricles of the brain, is one of the most understudied tissues in neuroscience. As it is becoming increasingly clear that this tiny structure plays a crucial role in health and disease of the central nervous system (CNS), it is of utmost importance to properly dissect the CP out of the brain ventricles in a way that allows downstream processing, ranging from functional to structural analysis. Here, isolation of the lateral and fourth brain ventricle mouse CP without the need for specialized tools or equipment is described. This isolation technique preserves the viability, function, and structure of cells within the CP. On account of its high vascularization, the CP can be visualized floating inside the ventricular cavities of the brain using a binocular microscope. However, transcardial perfusion required for downstream analysis can complicate the identification of the CP tissue. Depending on the further processing steps (e.g., RNA and protein analysis), this can be solved by visualizing the CP via transcardial perfusion with bromophenol blue. After isolation, the CP can be processed using several techniques, including RNA, protein, or single cell analysis, to gain further understanding on the function of this special brain structure. Here, scanning electron microscopy (SEM) on whole mount CP is used to get an overall view of the structure.

The choroid plexus (CP), an understudied tissue in neuroscience, plays a key role in health and disease of the central nervous system. This protocol describes a microdissection technique for isolating the CP and the use of scanning electron microscopy to obtain an overall view of its cellular structure.

小鼠脉络丛的显微切割和全安装扫描电子显微镜可视化

The choroid plexus (CP), a highly vascularized structure protruding into the ventricles of the brain, is one of the most understudied tissues in ...

脉络丛中的选择性基因沉默

Targeted Knockdown of Genes in the Choroid Plexus

The choroid plexus (ChP) serves as a critical gateway for immune cell infiltration into the central nervous system (CNS) under both physiological and pathological conditions. Recent research has shown that regulating ChP activity may offer protection against CNS disorders. However, studying the biological function of the ChP without affecting other brain regions is challenging due to its delicate structure. This study presents a novel method for gene knockdown in ChP tissue using adeno-associated viruses (AAVs) or cyclization recombination enzyme (Cre) recombinase protein consisting of TAT sequence (CRE-TAT). The results demonstrate that after injecting AAV or CRE-TAT into the lateral ventricle, the fluorescence was exclusively concentrated in the ChP. Using this approach, the study successfully knocked down the adenosine A2A receptor (A2AR) in the ChP using RNA interference (RNAi) or Cre/locus of X-overP1 (Cre/LoxP) systems, and showed that this knockdown could alleviate the pathology of experimental autoimmune encephalomyelitis (EAE). This technique may have important implications for future research on the ChP's role in CNS disorders.

作者聚焦：脉络丛研究中基因表达操作技术的见解和创新 

Here, we describe a method to selectively alter gene expressions in the choroid plexus while avoiding any impact in other brain areas.

脊索丛中基因的靶向敲除

The choroid plexus (ChP) serves as a critical gateway for immune cell infiltration into the central nervous system (CNS) under both physiological and ...