Name: a comprehensive protocol for manual segmentation of the medial temporal lobe structures
Uploaded: 2014-07-02T13:00:00.000+00:00
Duration: 12 min 30 s
Description: Watch this Scientific Journal Video about A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures at JoVE.com

This research was supported by funds to FD. MM was supported by an IGERT Fellowship under National Science Foundation Grant No. 0903622. The authors wish to thank the Dolcos Lab members for assistance with data collection and preparation.

1，杏仁核<ol><li>艾米的前片<ol><li>找出其中的阈限岛最初出现，那里的额叶和颞叶之间的白质连接是连续的，可见30的AMY的第一片。在冠状视图中，使用角包作为AMY的下侧壁边界。 </li><li>找到视交叉作为一个具有里程碑意义的AMY的外观。用轴向和矢状意见，从周围的钩回区分AMY在其早期片。跟随周边AMY白质束的轴向视图以排除内嗅区32。 </li><li>向后运动，识别第一切片，其中，前连合是贯穿两个半球28，其中AMY是其典型的形状可见连续的。使用嗅沟作为superomedial地界，从semianular sulcu眼底的假想线追踪逆时针AMY沿白质的AMY作为内下方边框，颞干的外侧缘，并回到嗅沟的下尖s到完成跟踪31。 </li></ol></li><li>在AMY的后片<ol><li>请注意，在这个层面上，无论是AMY和HC在同一个片（S）可见。 </li><li>仍然在冠状视图，识别AMY，其中结构优于内侧延伸侧脑室36的颞角（或alveus如果心室不存在）和横向于钩突回，突起的最后切片慧聪的头。检查的准确性和一致性跟踪的矢状和轴的意见。 </li><li>绘制的假想线从岛的下圆沟的眼底视神经束作为AMY 31，这也区分它从苍白球和壳核的灰质的上缘。 </li><li>沿迹半月回作为superomedial边框和排除钩突回32。使用侧脑室下角和横向划分的时间干。 </li></ol></li><li>在前后方向的AMY连续切片<ol><li>使用上述有关指引系统地跟踪AMY片逐片。在AMY的前部部分，使用相同的边界，作为最前片;相反，在AMY的后部，使用相同的边界作为最靠后的切片。 </li><li>继续聘请轴向和矢状面的意见，以帮助定义和进一步细化AMY边界。 </li></ol></li></ol> 2，海马<ol><li>本地化慧聪<ol><li>开始跟踪慧聪时，侧脑室颞角出现沿AMY的下侧壁边界。如果侧脑室颞角已经存在于前一个切片，注意，第Ë发病的HC，然后由侧脑室扩大和伸展superolaterally颞角来表示。 </li><li>结束的HC，其最后一个出场的内下方，以侧脑室31的三角跟踪。总是利用不同的观点，帮助本地化HC和它的边界。 </li></ol></li><li>慧聪的边界定义<ol><li>划定对颞角外侧HC。在情况下，侧脑室颞角是不够的感知，从分割排除的体素中的一个行来表示它。 </li><li> Inferiorly，使用束角（或其假想扩展名）的心室腔慧聪从PHG分开。使用alveus随着伞的上缘。在整个使用相同的定义跟踪慧聪。 </li><li>此外，包括下托插入分割，使得其内侧边界的PHG的白质束，优对齐与钩回的曲线，以及主要水平地从HC 37延伸。向后跟踪，维护这些定义，直到距状沟干预。 </li></ol></li><li>慧聪的注意到分部<ol><li>请注意，HC可分为三个部分：头部，身体和尾巴。 </li><li>使用钩回顶点的外观来标记从HC头向HC体的尺寸的过渡，并迅速升高和膨胀，这通常与穹窿的小腿的外观一致，以表示的HC尾巴的外观23,30,38。 </li></ol></li><li>跟踪以下结构时要特别注意。 <ol><li>包括在分割后钩回。 </li><li>省略脉络丛从在冠状切片的分割的alveus以上，虽然这可能是不可能的较低分辨率图像。 </li><li>指两个不同的观点，以避免包含了C的尾巴audate和枕在慧聪尾优越的方面。 </li><li>通过注意到其出现在穹窿，其中最初它是从海马尾部由片形吸虫灰霉病和更多分离的小腿的水平避免夹杂物的束状回的后部变成灰质优于距状沟32。 </li></ol></li></ol><img alt="图2" fo:content-width="4in" src="/files/ftp_upload/50991/50991fig2highres.jpg" width="400" /> 图2。 使用本协议，显示出大脑中的实际位置跟踪的现代货箱码头，并在其主要结构的相对位置的一位代表矢状切片， 即 AMY（红色），HC（蓝色），中国（黄色），在ERC（粉红色），和初级卫生保健（绿色）。 3，海马旁回<ol><li>对PHG的注意到分部<ol><li>注意，PHG约n为分为两个主要部分：前PHG（ 即中国和ERC），和后PHG（ 即 PHC）。 </li><li>请注意，在所述前部部分，在中国出现早于ERC，并通过其整个过程横向侧翼它。 </li><li>在ERC消失后，注意到，中国涵括其对PHG的地方，并继续对3毫米。 </li><li>超出了这个段，跟踪后PHG，其中PHC接管PHG的宽度，直到其端部30。 </li></ol></li><li>对PHG的前片<ol><li>定义中国的第一片与CS 25,39的出现。在ERC来临之前，跟踪中国从内侧边缘在CS的横向银行对施瓦尔贝的回的横向眼底，或内侧之一，如果存在施瓦尔贝两回，或的中点在没有这个回25,39背temporopolar表面。 </li><li>开始追查ERC 5 mm的内六角圆柱的阈限岛40,41。 </li><li>继续使用内侧temporopolar沟作为优良端40的眼底，以及半环形沟的眼底的AMY出现之后，或在转角束的假想延伸满足心室腔，如果半环形沟是点跟踪ERC区分25。请注意，它延伸inferiorly直接满足心室腔或软脑膜表面。 </li><li>中国与ERC之间的边界可能会有所不同切片切片。 <ol><li>当CS为深 （≥1.5公分），从内侧缘此沟的内侧银行追查中国，其横向银行25的中点。 </li><li>在一个普通的 CS（深度为1-1.5厘米）的情况下，跟踪中国从抵押品沟的沟25的侧堤的内侧端部的内侧银行的中点的区域。 </li><li>以&lt;EM&gt;浅CS（&lt;1公分），跟踪中国从这个沟的眼底的梭状回25冠的中点。 </li></ol></li><li>当CS被中断，通常在钩回顶点的水平，通过新兴从其眼底小回，跟踪中国向外侧沟25的眼底。包括或根据目标投资回报率不包括白质。 </li><li>跟踪ERC直到1.5毫米后的钩回顶点，或回intralimbicus 42月底。 </li><li>延长中国的跟踪内侧占据ERC其终止，在后者的定义一直持续到4.5毫米后适用于钩回顶点，或回intralimbicus 42结束后的地方。中国然后由PHC 25,30被取代。 </li></ol></li><li>对PHG的后片<ol><li>开始跟踪PHC对切片后至中国的末尾，直到4毫米后到t他最后的HC尾32。从文献的替代定义在讨论部分进行了描述。同样，包含或排除根据目标白质。 </li><li>使用ERC消失后中国的后部所描述的同样的方法描出初级卫生保健。也可以使用扣带的白质为上缘，一旦它出现。继续跟踪，以这种方式，直到距状沟，这superomedially限制了初级卫生保健的沟30的下边缘的外观。 </li><li>如果一个小沟出现在距状沟的出现之前，它包括在分割，但在从距状沟区分它谨慎。 </li></ol></li></ol>

The authors have no conflicts of interest to declare.

传统上，手动分割一直被认为是黄金标准被许多研究者。尽管如此，个别结构的精确划定变得复杂化了MTL结构的高度可变的形态，并通过对周围神经组织和非神经领域这些结构的通常弱的MRI对比。从历史上看，有在文献中已经描述冲突的一些MTL结构。在某些情况下，分割中国，例如，抵押品沟已被描述为中断40,41，但这种先前已在其他文献中描述为一个短的CS不超过该阈限insulae 30?...

A correction was made to <a href="/video/50991">A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures</a>. Table 1 and its legend were updated. References 10 and 14 were also updated.
The references were updated from:
<ol start="10">
<li>Wager, T. D. &amp; Smith, E. E. Neuroimaging studies of working memory: a meta-analysis. Cognitive, Affective &amp; Behavioral Neuroscience. 3(4), 255-274 (2003).</li>
</ol>
<ol start="14">
<li>Scheltens, Ph, et al. Atrophyofmedialtemporallobeson MRIin 'probable' Alzheimer's disease and normal ageing: diagnostic value and neuropsychological correlates. Journal of Neurology, Neurosurgery, and Psychiatry. 55(10), 967-972, (1992).</li>
</ol>
to:
<ol start="10">
<li>Wager, T. D., Phan, K. L., Liberzon, I., &amp; Taylor, S. F. Valence, gender, and lateralization of functional brain anatomy in emotion: a meta-analysis of findings from neuroimaging. Neuroimage. 19 (3), 513-31, doi:10.1016/S1053-8119(03)00078-8 (2003).</li>
</ol>
<ol start="14">
<li>de Leon, M. J. et al. Imaging and CSF studies in the preclinical diagnosis of Alzheimer's disease. Annals of the New York Academy of Sciences. 1097, 114-145, doi:10.1196/annals.1379.012 (2007).</li>
</ol>
Table 1 had its legend updated from:
Table 1. Representative volumetric results of the bilateral AMY and the HC of a single subject, from manual tracing using the present protocol and automatic segmentation. Automatic segmentation has underestimated the volume of each of the four structures compared. Corrected volume was calculated as the ratio between Voxel volume and Intracranial volume (ICV). For this subject, ICV = 1446616.73 mm3.
to:
Table 1. Representative volumetric results of the bilateral AMY and the HC of a single subject, from manual tracing using the present protocol and automatic segmentation. Automatic segmentation has misestimated the volume of each of the four structures compared. Corrected volume was calculated as the ratio between Voxel volume and ICV. For this subject, ICV = 1599482.11 mm3. <a href="http://www.jove.com/files/ftp_upload/50991/50991table1.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

A correction was made to <a href="/video/50991">A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures</a>. Table 1 and its legend were updated. References 10 and 14 were also updated.

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

内侧颞叶（MTL），整合感觉信息1的最高水平假定的区域，一直有针对性的分析的常见主题。例如，海马和海马旁相关领域已被广泛研究记忆研究2-5。此外，杏仁核的作用已被频频强调研究探讨情绪加工与情感认知的相互作用6-11。最近，各种各样的现代货箱码头地区也受到了关注个性神经，连接这些和其他脑区的结构和功能在个体的人格特质差异12的新兴领域。评估MTL结构的解剖和功能可促进退行性疾病，其中具体结构和功能异常可发生在不同的现代货箱码头结构的诊断是非常重要的。例如，在阿尔茨海默病（AD），显著一个内嗅皮质和海马的奖杯可以观察到13,14，和海马萎缩可预测从轻度认知损害转变到AD 15。最近的自动分割算法已成为流行的分割皮层和皮层下结构，但与任何工具，这些程序不可避免地在某些情况下会发生错误。在这样的情况下研究者应配备两个的知识和指导方针，识别MTL结构的解剖边界。在现存文献的趋势已经针对个别MTL次区域16-21，有许多协议趋向于集中在海马16-19。 不像大多数的现代货箱跟踪可用的出版方针，本协议提供了一套全面的指引，让所有MTL次区域的清晰定位。以下MTL结构跟踪指导方针进行了说明：杏仁核（AMY），海马（HC），边缘皮层（中国），内嗅皮层（ERC）和旁海马皮层（PHC）。阿美与慧聪首先追查，并再其次是海马旁回（PHG）的结构。注意，通称HC此处用来指对HC的形成，这包括对HC正确，下托，以及在钩回22-24的后段。还请注意，PHG可以分为两部分，前部和后部部分。内PHG的前部，它可以进一步分为外侧和内侧前PHG，其皮层区域对应于中国及ERC，分别。在PHC中，PHG的后侧部分的皮层区域，对应于海马旁皮质正确。为简单起见，我们将使用术语中国和ERC来指外侧和内侧前PHG，和PHC指后PHG。该segme陈述的每个结构始于一个粗定位的前部和后部的边界，以及其他相关的地标，然后接着在冠状面切片进行逐片的实际跟踪，在一个anterior-posterior/rostro-caudal方向。在所有情况下，矢状和轴部分密切监控，以协助解剖界限和标志性建筑的本土化。 需要这样的跟踪准则还示出在数字显示的自动和手动分割协议的输出之间可能存在的差异。一种协议，它描述了所有的MTL结构在当前视觉格式的优点是在变化的解剖结构（ 例如，抵押品沟[CS]深度），可以影响边界定义可以在上下文中与周围的解剖结构（将描述如中国和ERC内侧和外侧边界的位置，具体取决于在CS 25的深度</s达&gt;）。这可能不是很清楚或可理解为一个没有经验的示踪剂或有经验的示踪剂谁只跟踪单个或独立的结构，并且据我们所知，这种视觉上全面指引不存在。 本协议是在以前的调查，查明差贡献MTL次区域情感26的记忆增强的效果，适用于最近的事态发展在结构磁共振（MR）成像允许更高分辨率的脑图像用于现代货箱跟踪指导方针明确简报。跟踪说明从健康志愿者（女，24岁）获得的扫描，使用的是3T磁共振扫描仪。解剖图像被收购的3D MPRAGE（TR = 1800毫秒，TE = 2.26毫秒; FOV = 256×256毫米，体素大小= 1×0.5×0.5毫米），角平行于AC-PC的收购。如果图像数据被获取具有不同的获取角度，如倾斜取向，该数据应该是章ridded以平行或垂直的方向，以AC-PC，使得解剖标志的描述翻译适当。该图像，然后翻译成NIFTI格式和输入分割软件27手动跟踪。在目前的协议中使用的扫描数据被收集作为被批准的机构审查委员会的一项研究的一部分，并提供了书面同意的志愿者。 通过各种不同的协议跟踪这些结构18-22,28-31，以及从解剖分析和地图集23,32,33图纸信息，本协议提出了一套全面的指引，解决矛盾的现存文献。通过随附的视觉材料的补充，这项工作有望推动现代货箱结构更清晰的认识，并挑起未来的研究兴趣在采用手动分割，无论是作为现代货箱追踪的主要方法还是作为supplementaRy的方法来自动分割。通过提供对于理解现代货箱解剖准确，直观，方便的指南，该协议将有助于研究人员识别出所有MTL次区域的位置，相对于其相邻的结构，即使只有一些MTL结构是专门针对分析。这不仅会增加定位精度，也有利于示踪剂作出明智的决定在形态变异，这是极有可能在MTL的案件。这些准则可以适用于研究涉及MTL的结构和/或功能性磁共振成像研究，包括体积分析和脑异常检测，以及用于功能，解剖定位程序，并tractographic分析，在健康组。本协议也可以被用于通知MTL结构分割为患者（ 例如 ，患有萎缩），如果主要解剖标志相对保留。追踪临床学科s&#39;的数据可以采取额外的时间和精力，这取决于萎缩和/或解剖结构变化的严重程度。 定义的ROI时，需要考虑脑回和皮层之间的区别是很重要的。在解剖学上，带回这里指的是白质和灰质，而皮质指事只有灰色。根据不同的使用目的的投资回报率，分割可能包括白质或排除它。 我们建议跟踪按顺序进行，由子子，一个半球的时间。某些软件程序包34允许跟踪概述了一个片被粘贴到随后的切片，一个功能，可以加速这个过程的边界。它始终是最好根据需要来参考相对的半球，以便检查整个双方一致（ 例如 ，在检测的解剖学界标）。或者，平行两半球内的相同结构的跟踪S可同时被执行。不管跟踪是否串行或并行，一旦这个过程完成后，示踪剂应仔细检查最终结果，并根据需要进行调整，参照两半球​​和多平面意见。取决于示踪剂的经验和成像数据的分辨率，对MTL为健康受试者数据的手动分段可以从8-10小时或更多，在一个新手示踪剂的情况下，以3-4小时，在情况的经验之一。 <img alt="图1" fo:content-width="4in" src="/files/ftp_upload/50991/50991fig1highres.jpg" width="400" /> 图1。一个3D概述现代货箱码头，利用本协议的追踪。此处所示的结构是AMY（红色），HC（蓝色），中国（黄色），在ERC（粉红色），和初级卫生保健（绿色） 。

<table><tbody><tr><td>ITK-SNAP</td><td>ITK-SNAP Team at University of Pennsylvania and University of Utah</td><td>ITK-SNAP v2.2</td><td></td></tr><tr><td>FSL</td><td>Functional Magnetic Resonance Imaging of the Brain (FMRIB) Analysis Group</td><td>FSL v4.1</td><td></td></tr><tr><td>Siemens Magnetom Trio 3T MR Scanner</td><td>Siemens</td><td>Magnetom Trio 3T</td><td></td></tr></tbody></table>

a comprehensive protocol for manual segmentation of the medial temporal lobe structures

本论文描述了一个全面的协议集的大脑区域包括内侧颞叶（MTL）的手动跟踪：杏仁核，海马，以及相关的海马旁区（嗅， 嗅和海马旁适当）。可不像其他大多数跟踪协议，通常专注于某些MTL领域（ 如杏仁核和/或海马），通过跟踪目前的指导方针综合的角度允许所有MTL次区域的清晰定位。通过从不同的来源，其中包括现存的跟踪协议分别针对不同MTL结构，组织学报告和脑地图集，并用说明性的视觉材料的补充整合信息，本协议为了解准确，直观，方便的引导MTL解剖。需要这样的跟踪指引还示出了由自动和手动分割协议之间可能存在的差异强调。这种知​​识可以走向不仅涉及结构的MRI调查研究可以应用，而且结构功能的共存与fMRI信号的提取从解剖学上定义的ROI，在健康和临床组的一致好评。

插图手动和自动分割之间可能存在的差异的 手动分割为AMY，慧聪，中国，ERC和肝癌的三维模型如图1所示，和分割的矢状切面示于图2。为了说明手动和自动之间极端的可能差异的目的描记中，艾米从与错误自动分割代表受切片并列手动跟踪（见下图3）。虽然自动分割软件能够识别该结构的核心机构，其分割是相当粗糙的，?...

Watch this Scientific Journal Video about A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures at JoVE.com

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

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, ...

a-comprehensive-protocol-for-manual-segmentation-medial-temporal-lobe

Research

JoVE Journal

Neuroscience

20.2K 次观看.  University of Illinois Urbana-Champaign. 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.

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

The NeuroStar TMS Device: Conducting the FDA Approved Protocol for Treatment of Depression

The Neuronetics NeuroStar Transcranial Magnetic Stimulation (TMS) System is a class II medical device that produces brief duration, pulsed magnetic fields. These rapidly alternating fields induce electrical currents within localized, targeted regions of the cortex which are associated with various physiological and functional brain changes.1,2,3
In 2007, O'Reardon et al., utilizing the NeuroStar device, published the results of an industry-sponsored, multisite, randomized, sham-stimulation controlled clinical trial in which 301 patients with major depression, who had previously failed to respond to at least one adequate antidepressant treatment trial, underwent either active or sham TMS over the left dorsolateral prefrontal cortex (DLPFC). The patients, who were medication-free at the time of the study, received TMS five times per week over 4-6 weeks.4
The results demonstrated that a sub-population of patients (those who were relatively less resistant to medication, having failed not more than two good pharmacologic trials) showed a statistically significant improvement on the Montgomery-Asberg Depression Scale (MADRS), the Hamilton Depression Rating Scale (HAMD), and various other outcome measures. In October 2008, supported by these and other similar results5,6,7, Neuronetics obtained the first and only Food and Drug Administration (FDA) approval for the clinical treatment of a specific form of medication-refractory depression using a TMS Therapy device (FDA approval K061053).
In this paper, we will explore the specified FDA approved NeuroStar depression treatment protocol (to be administered only under prescription and by a licensed medical profession in either an in- or outpatient setting).

In this article, we examine the methodology and considerations relevant to the FDA approved depression treatment protocol using the Neuronetics NeuroStar TMS device.

NeuroStar TMS的设备进行美国FDA批准用于治疗抑郁症的议定书“

The Neuronetics NeuroStar Transcranial Magnetic Stimulation (TMS) System is a class II medical device that produces brief duration, pulsed magnetic ...

科研

神经科学

Calcium Imaging of Odor-evoked Responses in the Drosophila Antennal Lobe

The antennal lobe is the primary olfactory center in the insect brain and represents the anatomical and functional equivalent of the vertebrate olfactory bulb1-5. Olfactory information in the external world is transmitted to the antennal lobe by olfactory sensory neurons (OSNs), which segregate to distinct regions of neuropil called glomeruli according to the specific olfactory receptor they express. Here, OSN axons synapse with both local interneurons (LNs), whose processes can innervate many different glomeruli, and projection neurons (PNs), which convey olfactory information to higher olfactory brain regions.
Optical imaging of the activity of OSNs, LNs and PNs in the antennal lobe - traditionally using synthetic calcium indicators (e.g. calcium green, FURA-2) or voltage-sensitive dyes (e.g. RH414) - has long been an important technique to understand how olfactory stimuli are represented as spatial and temporal patterns of glomerular activity in many species of insects6-10. Development of genetically-encoded neural activity reporters, such as the fluorescent calcium indicators G-CaMP11,12 and Cameleon13, the bioluminescent calcium indicator GFP-aequorin14,15, or a reporter of synaptic transmission, synapto-pHluorin16 has made the olfactory system of the fruitfly, Drosophila melanogaster, particularly accessible to neurophysiological imaging, complementing its comprehensively-described molecular, electrophysiological and neuroanatomical properties2,4,17. These reporters can be selectively expressed via binary transcriptional control systems (e.g. GAL4/UAS18, LexA/LexAop19,20, Q system21) in defined populations of neurons within the olfactory circuitry to dissect with high spatial and temporal resolution how odor-evoked neural activity is represented, modulated and transformed22-24.
Here we describe the preparation and analysis methods to measure odor-evoked responses in the Drosophila antennal lobe using G-CaMP25-27. The animal preparation is minimally invasive and can be adapted to imaging using wide-field fluorescence, confocal and two-photon microscopes.

Calcium Imaging of Odor-evoked Responses in the Drosophila Antennal Lobe

We describe an established technique to measure and analyze odor-evoked calcium responses in the antennal lobe of living Drosophila melanogaster.

在气味诱发反应的钙成像果蝇触角叶

The antennal lobe is the primary olfactory center in the insect brain and represents the anatomical and functional equivalent of the vertebrate olfactory ...

Preparation of Parasagittal Slices for the Investigation of Dorsal-ventral Organization of the Rodent Medial Entorhinal Cortex

Computation in the brain relies on neurons responding appropriately to their synaptic inputs. Neurons differ in their complement and distribution of membrane ion channels that determine how they respond to synaptic inputs. However, the relationship between these cellular properties and neuronal function in behaving animals is not well understood. One approach to this problem is to investigate topographically organized neural circuits in which the position of individual neurons maps onto information they encode or computations they carry out1. Experiments using this approach suggest principles for tuning of synaptic responses underlying information encoding in sensory and cognitive circuits2,3.
The topographical organization of spatial representations along the dorsal-ventral axis of the medial entorhinal cortex (MEC) provides an opportunity to establish relationships between cellular mechanisms and computations important for spatial cognition. Neurons in layer II of the rodent MEC encode location using grid-like firing fields4-6. For neurons found at dorsal positions in the MEC the distance between the individual firing fields that form a grid is on the order of 30 cm, whereas for neurons at progressively more ventral positions this distance increases to greater than 1 m. Several studies have revealed cellular properties of neurons in layer II of the MEC that, like the spacing between grid firing fields, also differ according to their dorsal-ventral position, suggesting that these cellular properties are important for spatial computation2,7-10.
Here we describe procedures for preparation and electrophysiological recording from brain slices that maintain the dorsal-ventral extent of the MEC enabling investigation of the topographical organization of biophysical and anatomical properties of MEC neurons. The dorsal-ventral position of identified neurons relative to anatomical landmarks is difficult to establish accurately with protocols that use horizontal slices of MEC7,8,11,12, as it is difficult to establish reference points for the exact dorsal-ventral location of the slice. The procedures we describe enable accurate and consistent measurement of location of recorded cells along the dorsal-ventral axis of the MEC as well as visualization of molecular gradients2,10. The procedures have been developed for use with adult mice (&gt; 28 days) and have been successfully employed with mice up to 1.5 years old. With adjustments they could be used with younger mice or other rodent species. A standardized system of preparation and measurement will aid systematic investigation of the cellular and microcircuit properties of this area.

We describe procedures for preparation and electrophysiological recording from brain slices that maintain the dorsal-ventral axis of the medial entorhinal cortex (MEC). Because neural encoding of location follows a dorsal-ventral organization within the MEC, these procedures facilitate investigation of cellular mechanisms important for navigation and memory.

背腹鼠​​类内侧嗅皮层组织的调查矢状窦片的制备

Computation in the brain relies on neurons responding appropriately to their synaptic inputs. Neurons differ in their complement and distribution of ...

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 ...

Lesion Explorer: A Video-guided, Standardized Protocol for Accurate and Reliable MRI-derived Volumetrics in Alzheimer's Disease and Normal Elderly

Obtaining in vivo human brain tissue volumetrics from MRI is often complicated by various technical and biological issues. These challenges are exacerbated when significant brain atrophy and age-related white matter changes (e.g. Leukoaraiosis) are present. Lesion Explorer (LE) is an accurate and reliable neuroimaging pipeline specifically developed to address such issues commonly observed on MRI of Alzheimer's disease and normal elderly. The pipeline is a complex set of semi-automatic procedures which has been previously validated in a series of internal and external reliability tests1,2. However, LE's accuracy and reliability is highly dependent on properly trained manual operators to execute commands, identify distinct anatomical landmarks, and manually edit/verify various computer-generated segmentation outputs.
LE can be divided into 3 main components, each requiring a set of commands and manual operations: 1) Brain-Sizer, 2) SABRE, and 3) Lesion-Seg. Brain-Sizer's manual operations involve editing of the automatic skull-stripped total intracranial vault (TIV) extraction mask, designation of ventricular cerebrospinal fluid (vCSF), and removal of subtentorial structures. The SABRE component requires checking of image alignment along the anterior and posterior commissure (ACPC) plane, and identification of several anatomical landmarks required for regional parcellation. Finally, the Lesion-Seg component involves manual checking of the automatic lesion segmentation of subcortical hyperintensities (SH) for false positive errors.
While on-site training of the LE pipeline is preferable, readily available visual teaching tools with interactive training images are a viable alternative. Developed to ensure a high degree of accuracy and reliability, the following is a step-by-step, video-guided, standardized protocol for LE's manual procedures.

Lesion Explorer (LE) is a semi-automatic, image-processing pipeline developed to obtain regional brain tissue and subcortical hyperintensity lesion volumetrics from structural MRI of Alzheimer's disease and normal elderly. To ensure a high level of accuracy and reliability, the following is a video-guided, standardized protocol for LE's manual procedures.

病变资源管理器：一个视频引导，标准化为老年痴呆症准确，可靠的MRI衍生Volumetrics和正常老年人协议

Obtaining in vivo human brain tissue volumetrics from MRI is often complicated by various technical and biological issues. These challenges are ...

医学

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 ...

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 ...

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. We have developed a software package for accurate and robust shape modeling and group-wise analysis. Here, we introduce an pipeline for the shape analysis, from individual 3D shape modeling to quantitative group shape analysis. We also describe the pre-processing and segmentation steps using open software packages. This practical guide would help researchers save time and effort in 3D shape analysis on brain structures.

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

脑结构三维形状建模与分析

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. ...

加强脑部疾病的神经影像学分析

Manual Segmentation of the Human Choroid Plexus Using Brain MRI

The choroid plexus has been implicated in neurodevelopment and a range of brain disorders. Evidence demonstrates that the choroid plexus is critical for brain maturation, immune/ inflammatory regulation, and behavioral/cognitive functioning. However, current automated neuroimaging segmentation tools are poor at accurately and reliably segmenting the lateral ventricle choroid plexus. Furthermore, there is no existing tool that segments the choroid plexus located in the third and fourth ventricles of the brain. Thus, a protocol delineating how to segment the choroid plexus in the lateral, third, and fourth ventricle is needed to increase the reliability and replicability of studies examining the choroid plexus in neurodevelopmental and brain disorders. This protocol provides detailed steps to create separately labeled files in 3D Slicer for the choroid plexus based on DICOM or NIFTI images. The choroid plexus will be manually segmented using the axial, sagittal, and coronal planes of T1w images making sure to exclude voxels from gray or white matter structures bordering the ventricles. Windowing will be adjusted to assist in the localization of the choroid plexus and its anatomical boundaries. Methods for assessing accuracy and reliability will be demonstrated as part of this protocol. Gold standard segmentation of the choroid plexus using manual delineations can be used to develop better and more reliable automated segmentation tools that can be openly shared to elucidate changes in the choroid plexus across the lifespan and within various brain disorders.

作者聚焦：弥合解剖学差距并为算法研究奠定基础 

Despite the crucial role of the choroid plexus in the brain, neuroimaging studies of this structure are scarce due to the lack of reliable automated segmentation tools. The present protocol aims to ensure gold-standard manual segmentation of the choroid plexus that can inform future neuroimaging studies.

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 ...

一个全面协议的内侧颞叶结构的手动分割

摘要

探索更多视频

此视频中的章节

NeuroStar TMS的设备进行美国FDA批准用于治疗抑郁症的议定书“

在气味诱发反应的钙成像果蝇触角叶

背腹鼠类内侧嗅皮层组织的调查矢状窦片的制备

手动排水的斑马鱼胚胎脑室

病变资源管理器：一个视频引导，标准化为老年痴呆症准确，可靠的MRI衍生Volumetrics和正常老年人协议

高分辨率

t1 加权 mri 图像中皮质灰质的自动分割

脑结构三维形状建模与分析

使用脑部 MRI 手动分割人脉络丛

使用脑部 MRI 手动分割人脉络丛

一个全面协议的内侧颞叶结构的手动分割

摘要

探索更多视频

此视频中的章节

NeuroStar TMS的设备进行美国FDA批准用于治疗抑郁症的议定书“

在气味诱发反应的钙成像果蝇触角叶

背腹鼠​​类内侧嗅皮层组织的调查矢状窦片的制备

手动排水的斑马鱼胚胎脑室

病变资源管理器：一个视频引导，标准化为老年痴呆症准确，可靠的MRI衍生Volumetrics和正常老年人协议

高分辨率

t1 加权 mri 图像中皮质灰质的自动分割

脑结构三维形状建模与分析

使用脑部 MRI 手动分割人脉络丛

使用脑部 MRI 手动分割人脉络丛

背腹鼠类内侧嗅皮层组织的调查矢状窦片的制备