Object-based representation and analysis of light and electron microscopic volume data using Blender
Object-based representation and analysis of light and electron microscopic volume data using Blender
复制标题
使用 Blender 对光和电子显微体积数据进行基于对象的表示和分析
作者：
Albina Asadulina;Markus Conzelmann;Elizabeth A. Williams;Aurora Panzera;G. Jékely
光学和电子显微镜成像技术的快速改进和3D解剖图谱的开发需要新的方法来可视化和分析图像数据。原始光学显微镜数据的基于像素的表示受到可以同时可视化的通道数量的限制。来自大组织体积的复杂电子显微镜重建也具有可视化和分析的挑战性。在这里，我们利用开源平台Blender的高级可视化功能和灵活性来可视化和分析解剖图谱。我们使用光学显微镜为基础的基因表达图谱和电子显微镜连接体体积数据从幼虫阶段的海洋环节动物Platynereis dumerilii。我们在Blender中构建了基于对象的幼虫基因表达图谱，并开发了注释和共表达分析工具。我们还代表和分析连接体数据，包括神经元重建和潜在的突触连接。我们展示了Blender用于可视化和探索复杂解剖图谱的功能和灵活性。我们已经开发的资源，为Platynereis将促进数据共享和标准化的解剖图谱为这个物种。Blender的灵活性，特别是其嵌入式Python应用程序编程接口，意味着我们的方法可以很容易地扩展到其他生物体。
Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based representations of raw light microscopy data suffer from limitations in the number of channels that can be visualized simultaneously. Complex electron microscopic reconstructions from large tissue volumes are also challenging to visualize and analyze. Here we exploit the advanced visualization capabilities and flexibility of the open-source platform Blender to visualize and analyze anatomical atlases. We use light-microscopy-based gene expression atlases and electron microscopy connectome volume data from larval stages of the marine annelid Platynereis dumerilii. We build object-based larval gene expression atlases in Blender and develop tools for annotation and coexpression analysis. We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity. We demonstrate the power and flexibility of Blender for visualizing and exploring complex anatomical atlases. The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species. The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.
影响因子：
48
作者：
Ronneberger, Olaf;Liu, Kun;Driever, Wolfgang
通讯作者：
Driever, Wolfgang