DOI: 10.6084/m9.figshare.5500234.v1
title: Coordinate files of skeletonized wire models showing the structure of frontal cortex tissue of adult human brain

description: 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.