NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity.
NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity.
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DOI：
10.3389/fnana.2018.00059
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发表时间：
2018
影响因子：
2.9
通讯作者：
Knott G
中科院分区：
文献类型：
--
作者：
Jorstad A;Blanc J;Knott G
轴突、树突及其突触连接的几何形状提供了有关其功能特性的重要信息。这些可以直接从一系列电子显微镜图像的测量中收集。然而，手动和自动分割方法也可以产生大而准确的神经元结构模型，从中可以在3D空间中收集形态测量数据。这篇技术论文介绍了一系列软件工具，在Blender开源软件中运行，用于轴突及其突触连接的定量分析。这些允许用户注释串行EM图像以生成不同细胞结构的模型，或对在其他软件中生成的模型进行测量。这篇论文解释了这些工具是如何沿着轴突的长度定期测量横截表面积的，以及与周围神经细胞元素接触的数量，以及它所包含的细胞器（如囊泡和线粒体）的密度。在三维空间中，也可以在任何特征之间进行最近距离测量。这提供了许多功能，如钮扣检测和不同囊泡池大小的评估，允许用户全面描述轴突形态和连接的许多方面。
The geometries of axons, dendrites and their synaptic connections provide important information about their functional properties. These can be collected directly from measurements made on serial electron microscopy images. However, manual and automated segmentation methods can also yield large and accurate models of neuronal architecture from which morphometric data can be gathered in 3D space. This technical paper presents a series of software tools, operating in the Blender open source software, for the quantitative analysis of axons and their synaptic connections. These allow the user to annotate serial EM images to generate models of different cellular structures, or to make measurements of models generated in other software. The paper explains how the tools can measure the cross-sectional surface area at regular intervals along the length of an axon, and the amount of contact with other cellular elements in the surrounding neuropil, as well as the density of organelles, such as vesicles and mitochondria, that it contains. Nearest distance measurements, in 3D space, can also be made between any features. This provides many capabilities such as the detection of boutons and the evaluation of different vesicle pool sizes, allowing users to comprehensively describe many aspects of axonal morphology and connectivity.
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影响因子：
9.8
作者：
Belevich I;Joensuu M;Kumar D;Vihinen H;Jokitalo E
通讯作者：
Jokitalo E
影响因子：
10.6
作者：
Antiga, L;Steinman, DA
通讯作者：
Steinman, DA
影响因子：
3
作者：
Jorstad, Anne;Nigro, Biagio;Knott, Graham
通讯作者：
Knott, Graham
DOI：
10.1137/070692017
发表时间：
2008-10-13
期刊：
SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics
影响因子：
--
作者：
Kerr RA;Bartol TM;Kaminsky B;Dittrich M;Chang JC;Baden SB;Sejnowski TJ;Stiles JR
通讯作者：
Stiles JR
DOI：
10.1111/j.1365-2818.2005.01466.x
发表时间：
2005-04-01
期刊：
JOURNAL OF MICROSCOPY-OXFORD
影响因子：
--
作者：
Fiala, JC
通讯作者：
Fiala, JC