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Coordinate files of skeletonized wire models of 3D neural processes of the Drosophila brain hemisphere
dataset
posted on 2019-05-29, 13:31 authored by Rino Saiga, Ryuta MizutaniThis dataset contains coordinate files for skeletonized wire models of neuronal processes of the Drosophila brain hemisphere.
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.
Coordinates are divided into the files named on the basis of the z coordinate, which corresponds to the left-to-right direction of the brain. All files should be loaded to display the whole structure, but each file can be viewed individually to explore the local structure.
For more info: https://mizutanilab.github.io/
How to use .pdb files:
Viewer
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.
File format
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.
Three-dimensional coordinates
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.
Connection lines
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.
Constituent types
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.
Background of the related study:
A 3D analysis of the neural network of wild-type fruit flies Drosophila melanogaster Canton-S (Drosophila Genetic Resource Center, Kyoto Institute of Technology, Japan) was performed by synchrotron-radiation tomographic microscopy. X-ray absorption
coefficients were then used to construct the left half of the brain network, with the structural components used to model neuronal processes. Certain of these processes could be classified into groups that send long-range projections or repeated structures of the optic lobe, while unclassified structures were seen to correlate with neuronal processes contacts.
See the related publication linked from this data record for further detail on methodology.
