Structure of frontal cortex tissue of adult human brain

• Movie files
  
  • Three-dimensional rendering of electron densities. QuickTime(9.0 MB)
  • Skeletonized model. QuickTime(9.5 MB)
• Coordinate files
  
  • Release1.0.0(16 Jun 2010): This file contains five coordinate files. Each file describes skeletonized wire models of neurons and blood capillary vessels. 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.
  • Release0.9.0(3 Oct 2009): preliminary release, archived coordinate file of some structures.
• Reference
  Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Susumu Takekoshi, R. Yoshiyuki Osamura and Yoshio Suzuki (2010). Microtomographic analysis of neuronal circuits of human brain. Cerebral Cortex 20(7), 1739-1748. DOI PubMed pdf

3D micro structures of zebra fish and fruit fly

• Movie files
  
  • Three-dimensional rendering of juvenile zebra fish. QuickTime(10.8 MB)
  • Adult Drosophila melanogaster fruitfly. QuickTime(1.7 MB)
• Reference
  Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Susumu Takekoshi, R. Yoshiyuki Osamura and Yoshio Suzuki (2008). X-ray microtomogaphic imaging of three-dimensional structure of soft tissues. Tissue Engineering Part C 14(4), 359-363. DOI PubMed

Viewer
We recommend using the PC software 'MCTrace' for viewing the wire models of tissue microstructure. The MCTrace v2 can be downloaded from the MCTrace page.

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, several different 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. Wire models are 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'.

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 currently used 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.