Mizutani Lab 3D Structure Portal

Neuronal structures differ between individuals and the differences become extraordinary in schizophrenia.

Movie
3D neuronal network of a schizophrenia case YouTube
Reference
R Mizutani et al (2019). Three-dimensional alteration of neurites in schizophrenia. Transl. Psychiatry 9, 85. DOI pdf arXiv
R Mizutani et al (2021). Structural diverseness of neurons between brain areas and between cases. Transl. Psychiatry 11, 49. DOI pdf.

Three-dimensional structures of spinal cords and brains of a mouse model of multiple sclerosis

Movie
Three-dimensional rendering of brain hemisphere of a MS model mouse YouTube

Three-dimensional structure of spinal cord of a MS model mouse treated with fingolimod YouTube
Coordinate files
- Build 9 Dec 2018: This zip file contains 14 coordinate files and one Excel file. Each coordinate file contains Cartesian coordinate model of the spinal cord of MS model mouse or control mouse. The file name prefix represents the mouse ID in the paper. Statistics of the structural coordinates are summarized in the Excel file.
Reference
R Saiga et al. (2018). Synchrotron radiation microtomography of brain hemisphere and spinal cord of a mouse model of multiple sclerosis revealed a correlation between capillary dilation and clinical score. J. Comp. Neurol. in press. DOI arXiv PubMed

Three-dimensional X-ray visualization of mouse brain hemisphere

Movie
Three-dimensional rendering of the whole brain hemisphere
YouTube
Reference
R. Mizutani et al. (2016). Three-dimensional X-ray visualization of axonal tracts in mouse brain hemisphere. Sci. Rep. 6, 35061. DOI pdf arXiv

Three-dimensional network of Drosophila brain hemisphere

Movies

Three-dimensional rendering of absorption coefficients.
YouTube

Skeletonized model.
YouTube
Coordinate files
- Release 1.0.0 (Build 8 Jun 2012; DOI): This release contains five coordinate files. Each file describes skeletonized wire models of neuronal prcesses. Coordinates are divided into the files named on the basis of the z coordinate (such as 120608-zzzz.pdb), which corresponds to the left-to-right direction. All files should be loaded to display the whole structure, but each file can be viewed individually to explore the local structure.
Reference
R. Mizutani et al. (2013). Three-dimensional network of Drosophila brain hemisphere. J. Struct. Biol. 184(2), 271-279. DOI PubMed arXiv

Structure of frontal cortex tissue of adult human brain

Movies

Three-dimensional rendering of absorption coefficients.
YouTube

Skeletonized structures of neurons and blood vessels in the inner pyramidal and inner granular layers.
YouTube
Coordinate files
- Release 1.0.0 (Build 16 Jun 2010; DOI): This release 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 (i.e., 100616-zzzz.pdb), 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.
Reference
R. Mizutani et al. (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

Movies

Three-dimensional rendering of juvenile zebra fish.
YouTube

Adult Drosophila melanogaster fruitfly.
YouTube
Reference
R. Mizutani et al. (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 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 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.

Our micro-CT or nano-CT analysis is performed by recording x-ray images while rotating the sample. Then its 3D structure is reconstructed with the convolution back-projection method. This calculation is repeated for each tomographic slice, giving the 3D structure consisted of a large number of slices. Therefore, one 3D structure consists of thousands of images, usually in the 8-bit TIFF format. They are too large for the internet transfer, and it's impossible to place all the files online. So we provide them in DVD-ROMs if you would like. Please email mizutanilaboratory(at)gmail.com to request DVDs. They are provided at cost.