Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues
Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues
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DOI：
10.1002/cne.23852
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发表时间：
2016-01-01
影响因子：
2.5
通讯作者：
Magistretti, Pierre J.
中科院分区：
文献类型：
--
作者：
Cali, Corrado;Baghabra, Jumana;Magistretti, Pierre J.
电子显微镜（EM）应用于连续成像的进展为分析细胞结构的新方法打开了大门。手动和半自动分割的新的和改进的算法和工作流程使我们能够以前所未有的细节观察最小细胞特征的空间排列。从更大的样本中，可以生成更复杂的模型;然而，它们对数据管理和分析提出了新的挑战。在这里，我们回顾了一些目前可用的解决方案，并详细介绍了我们的方法。我们使用完全沉浸式虚拟现实（VR）环境CAVE（洞穴自动虚拟环境），一个我们能够投影细胞重建并以3D方式可视化的房间，进入用Blender创建的世界，Blender是一个免费的，完全可定制的3D建模软件，带有NeuroMorph插件，用于脑组织EM制备的可视化和分析。我们的工作流程允许使用ilastik（一种用于EM堆栈半自动分割的软件工具）全面快速重建脑神经元体积。有了这个可视化环境，我们可以走进包含神经元和星形胶质细胞过程的模型，研究糖原颗粒的空间分布，糖原颗粒是选择性储存在星形胶质细胞中的主要能量来源。CAVE的使用是观察糖原非随机分布的关键，并使我们开发了定量分析糖原聚集和与其他亚细胞特征接近的工具。(c)2015年威利期刊公司
Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. (c) 2015 Wiley Periodicals, Inc.