Coordinate files of skeletonized wire models showing the structure of frontal cortex tissue of adult human brain

This dataset contains coordinate files describing skeletonized wire models of neurons and blood capillary vessels of a human brain tissue. <br>Files are in the Protein Data Bank .pdb textual file format, containing atomic coordinates. Files can be previewed in their structural form via the MCTrace page at GitHub or in the figshare browser. Coordinates are openly accessible via text edit software.<br><br>Coordinates are divided into the files named on the basis of the z coordinate, which corresponds to the direction perpendicular to the brain surface. All files should be loaded to display the whole structure, but each file can be viewed individually to explore the local structure.<br>For more info: https://mizutanilab.github.io/<br><b>How to use .pdb files:</b><br><b>Viewer</b>We recommend using the PC software 'MCTrace' for viewing the wire models of tissue microstructure. The MCTrace can be downloaded from the MCTrace page at GitHub.<br><b>File format</b>All files are plain text files. Most of the lines are based on the PDB format, a well-known format for describing three-dimensional models of macromolecules. Therefore, PDB viewers can be used to display the model coordinates. However, the 'REMARK RM' lines for display control can be recognized only by MCTrace.<br><b>Three-dimensional coordinates</b>The first half of the file lines are HETATM entries. Each HETATM entry correspond to a 'node' of a wire model. The wire model is displayed by connecting these nodes. An HETATM entry consists of HETATM header, entry number, node identifier, constituent type, constituent identifier, xyz coordinates (in micrometers), density, and radius. The entry name HETATM is derived from 'hetero atom' of the original PDB format.<br><b>Connection lines</b>In the last half of the file, CONECT entries describe connections between node entries. Some PDB viewers including the program MCTrace can recognize the CONECT entries and display connections.<br><b>Constituent types</b>The three-dimensional tissue structure has many types of constituents. The constituent types of the human brain structure are: PYR, pyramidal neuron; STE, stellate neuron; ASY, aspiny stellate neuron; NEU, neuron; GLI, glial cell; UND, orphan neurites; CEL, uncategorized cell; and VES, blood vessels. The constituent type of other structures represents group names, which are determined on the basis of the three-dimensional structure.<br><b>Background of the related study:</b>The related study reports a 3D analysis of the neuronal circuits of human cerebral cortex. Neuronal circuits, which are essential for brain functions, are built up by neurons as a 3D network, so tracing the 3D neuronal network of human cerebral cortex is the first step to understanding the mechanism of human brain functions. The cortical microstructures were visualized by X-ray microtomographic imaging of adult frontal cortex tissue stained with metal impregnation. The skeletonized wire models in this dataset were built by tracing the 3D distribution of X-ray absorption coefficients. The obtained neuronal models were composed of 240 pyramidal neurons and 131 interneurons. Capillary vessel structures along with blood cells in the capillary lumen were also visualized and traced to build capillary network models.<br>See the related publication linked from this data record for further detail on methodology.

本数据集包含描述人类脑组织神经元与毛细血管骨架化线模型的坐标文件。<br>文件采用蛋白质数据银行（Protein Data Bank）.pdb纯文本格式，存储原子坐标。可通过GitHub上的MCTrace页面或figshare浏览器预览其结构，坐标可通过文本编辑软件公开访问。<br><br>坐标按z坐标命名分组，z轴对应垂直于大脑表面的方向。需加载全部文件以展示完整结构，也可单独查看各文件以探索局部结构。更多信息可访问：https://mizutanilab.github.io/<br><b>.pdb文件使用方法：</b><br><b>查看器</b>推荐使用PC端软件「MCTrace」查看组织微结构的线模型，MCTrace可从GitHub的MCTrace页面下载。<br><b>文件格式</b>所有文件均为纯文本文件，多数行遵循PDB格式——这是一种用于描述大分子三维模型的通用格式，因此可使用PDB查看器展示模型坐标。但仅MCTrace可识别用于显示控制的「REMARK RM」行。<br><b>三维坐标</b>文件前半部分为HETATM条目，每个HETATM条目对应线模型的一个「节点」。通过连接这些节点即可展示线模型。HETATM条目由HETATM标识、条目编号、节点标识符、组分类型、组分标识符、xyz坐标（单位：微米）、密度与半径组成。HETATM这一名称源自原始PDB格式中的「异原子（hetero atom）」。<br><b>连接行</b>文件后半部分的CONECT条目用于描述节点间的连接关系。包括MCTrace在内的部分PDB查看器可识别CONECT条目并展示连接关系。<br><b>组分类型</b>三维组织结构包含多种组分。人类大脑结构的组分类型包括：PYR（锥体细胞神经元，pyramidal neuron）、STE（星状神经元，stellate neuron）、ASY（无棘星状神经元，aspiny stellate neuron）、NEU（神经元，neuron）、GLI（神经胶质细胞，glial cell）、UND（游离神经突，orphan neurites）、CEL（未分类细胞，uncategorized cell）以及VES（血管，blood vessels）。其他结构的组分类型为基于三维结构确定的组名。<br><b>相关研究背景：</b>相关研究报道了人类大脑皮层神经元环路的三维分析。作为大脑功能的核心基础，神经元环路由神经元构建为三维网络，因此追踪人类大脑皮层的三维神经元网络是解析人类大脑功能机制的第一步。本研究通过金属浸渍染色的成年额叶皮层组织的X射线显微断层成像，实现皮层微结构的可视化。本数据集内的骨架化线模型通过追踪X射线吸收系数的三维分布构建得到。所获得的神经元模型包含240个锥体细胞神经元与131个中间神经元。同时还对毛细血管腔中的血管结构与血细胞进行可视化与追踪，以构建毛细血管网络模型。<br>有关方法学的详细信息，请参阅本数据记录关联的相关发表文献。