NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks
NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks
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DOI：
10.1007/s12021-014-9242-5
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发表时间：
2015-01-01
期刊：
影响因子：
3
通讯作者：
Knott, Graham
中科院分区：
文献类型：
--
作者：
Jorstad, Anne;Nigro, Biagio;Knott, Graham
连续电子显微镜成像对于探索细胞和组织的结构至关重要。块面扫描电子显微镜方法的发展及其捕获大图像堆栈的能力，其中一些具有近各向同性体素，被证明对脑组织的探索特别有用。这导致了许多算法和软件的创建，用于从图像堆栈中分割出不同的特征。然而，很少有工具可用于查看这些结果并对所有或部分这些3D模型进行详细的形态测量分析。我们已经解决了这个问题，通过构建一个集合的软件工具，称为NeuroMorph，用户可以查看分割结果，结合原始图像堆栈，在3D中操作这些对象，并进行任何区域的测量。这种收集形态测量数据的方法提供了一种更快的方法来分析结构的几何形状，如树突棘和轴突终扣。这弥合了计算机视觉研究提供的快速重建技术与目前使用手动分割方法从分割结构收集形状和形式测量值的需求之间存在的差距。
Serialelectron microscopy imaging is crucial for exploring the structure of cells and tissues. The development of block face scanning electron microscopy methods and their ability to capture large image stacks, some with near isotropic voxels, is proving particularly useful for the exploration of brain tissue. This has led to the creation of numerous algorithms and software for segmenting out different features from the image stacks. However, there are few tools available to view these results and make detailed morphometric analyses on all, or part, of these 3D models. We have addressed this issue by constructing a collection of software tools, called NeuroMorph, with which users can view the segmentation results, in conjunction with the original image stack, manipulate these objects in 3D, and make measurements of any region. This approach to collecting morphometric data provides a faster means of analysing the geometry of structures, such as dendritic spines and axonal boutons. This bridges the gap that currently exists between rapid reconstruction techniques, offered by computer vision research, and the need to collect measurements of shape and form from segmented structures that is currently done using manual segmentation methods.