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Three-dimensional reconstruction of brain structures of the rodent Octodon degus: a brain atlas constructed by combining histological and magnetic resonance images.

Kumazawa-Manita N, Katayama M, Hashikawa T, Iriki A - Exp Brain Res (2013)

Bottom Line: Degus (Octodon degus) are rodents that are becoming more widely used in the neuroscience field.However, relatively little information is known about the anatomy of degu brains.This manuscript describes the construction of a three-dimensional (3D) volume rendered model of the degu brain that combines histological and magnetic resonance images.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Symbolic Cognitive Development, RIKEN, Brain Science Institute, Wako, Saitama, 351-0198, Japan, nkuma@brain.riken.jp.

ABSTRACT
Degus (Octodon degus) are rodents that are becoming more widely used in the neuroscience field. Degus display several more complex behaviors than rats and mice, including complicated social behaviors, vocal communications, and tool usage with superb manual dexterity. However, relatively little information is known about the anatomy of degu brains. Therefore, for these complex behaviors to be correlated with specific brain regions, a contemporary atlas of the degu brain is required. This manuscript describes the construction of a three-dimensional (3D) volume rendered model of the degu brain that combines histological and magnetic resonance images. This atlas provides several advantages, including the ability to visualize the surface of the brain from any angle. The atlas also permits virtual cutting of brain sections in any plane and provides stereotaxic coordinates for all sections, to be beneficial for both experimental surgeries and radiological studies. The reconstructed 3D atlas is freely available online at: http://brainatlas.brain.riken.jp/degu/modules/xoonips/listitem.php?index_id=24 .

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A guide to using the “SG-eye 3D Atlas” software. The active buttons in the menu bar are labeled (1–10). The functions of these buttons are explained in the Electronic Supplementary material and can be visualized in the tooltip window. Coronal sections can be visualized by manipulating the bottom rightcorner panel (labeled A). Specifically, the boxes labeled “C” and “Move with” in the “Clipping” and “Plane” modes in the “Axial” tab must be clicked. The “C” slider can be moved to change levels along the rostro-caudal axis. The numbers indicated in the boxes to the right of the sliders are the distance in mm from the interaural zero line. These numbers are either positive or negative to signify the rostral and caudal positions relative to the zero line, respectively. Sagittal and horizontal sections can be obtained in a similar fashion (click the “S” box for sagittal, or the “H” box for horizontal). 3D image or outlines can be removed or added by clicking the appropriate buttons (labeled 6 and 7). MR images can also be visualized by clicking the appropriate button (labeled 8). Coordinate transformations can be performed in the “Free” tab in the bottom right control panel (labeled A). These transformations can be performed on any combination of Nissl sections, MRI planes, and outlines by clicking the appropriate buttons (labeled 2, 6, 7, and 8) and for any plane of sections by clicking the appropriate buttons (the C, S, and H buttons). The hierarchical organization of the brain structures is indicated in the middle right panel (labeled B). Representative structures are indicated with unique colors in the image
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Fig5: A guide to using the “SG-eye 3D Atlas” software. The active buttons in the menu bar are labeled (1–10). The functions of these buttons are explained in the Electronic Supplementary material and can be visualized in the tooltip window. Coronal sections can be visualized by manipulating the bottom rightcorner panel (labeled A). Specifically, the boxes labeled “C” and “Move with” in the “Clipping” and “Plane” modes in the “Axial” tab must be clicked. The “C” slider can be moved to change levels along the rostro-caudal axis. The numbers indicated in the boxes to the right of the sliders are the distance in mm from the interaural zero line. These numbers are either positive or negative to signify the rostral and caudal positions relative to the zero line, respectively. Sagittal and horizontal sections can be obtained in a similar fashion (click the “S” box for sagittal, or the “H” box for horizontal). 3D image or outlines can be removed or added by clicking the appropriate buttons (labeled 6 and 7). MR images can also be visualized by clicking the appropriate button (labeled 8). Coordinate transformations can be performed in the “Free” tab in the bottom right control panel (labeled A). These transformations can be performed on any combination of Nissl sections, MRI planes, and outlines by clicking the appropriate buttons (labeled 2, 6, 7, and 8) and for any plane of sections by clicking the appropriate buttons (the C, S, and H buttons). The hierarchical organization of the brain structures is indicated in the middle right panel (labeled B). Representative structures are indicated with unique colors in the image

Mentions: The newly developed “SG-eye” software was used for 3D volume rendering of two-dimensional (2D) data (Fiatlux, Tokyo, Japan). SG-eye constructs 3D models by surface rendering and GPU accelerated volume ray-casting. The volume ray-casting algorithm consists of four steps: ray-casting, sampling, shading, and compositing. In the ray-casting step, a ray of sight is cast through the entire volume for each pixel. SG-eye contains several additional functions including position-adjusting, editing of mask images, and labeling and annotating brain regions. The SG-eye operating guide is explained in Fig. 5.


Three-dimensional reconstruction of brain structures of the rodent Octodon degus: a brain atlas constructed by combining histological and magnetic resonance images.

Kumazawa-Manita N, Katayama M, Hashikawa T, Iriki A - Exp Brain Res (2013)

A guide to using the “SG-eye 3D Atlas” software. The active buttons in the menu bar are labeled (1–10). The functions of these buttons are explained in the Electronic Supplementary material and can be visualized in the tooltip window. Coronal sections can be visualized by manipulating the bottom rightcorner panel (labeled A). Specifically, the boxes labeled “C” and “Move with” in the “Clipping” and “Plane” modes in the “Axial” tab must be clicked. The “C” slider can be moved to change levels along the rostro-caudal axis. The numbers indicated in the boxes to the right of the sliders are the distance in mm from the interaural zero line. These numbers are either positive or negative to signify the rostral and caudal positions relative to the zero line, respectively. Sagittal and horizontal sections can be obtained in a similar fashion (click the “S” box for sagittal, or the “H” box for horizontal). 3D image or outlines can be removed or added by clicking the appropriate buttons (labeled 6 and 7). MR images can also be visualized by clicking the appropriate button (labeled 8). Coordinate transformations can be performed in the “Free” tab in the bottom right control panel (labeled A). These transformations can be performed on any combination of Nissl sections, MRI planes, and outlines by clicking the appropriate buttons (labeled 2, 6, 7, and 8) and for any plane of sections by clicking the appropriate buttons (the C, S, and H buttons). The hierarchical organization of the brain structures is indicated in the middle right panel (labeled B). Representative structures are indicated with unique colors in the image
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig5: A guide to using the “SG-eye 3D Atlas” software. The active buttons in the menu bar are labeled (1–10). The functions of these buttons are explained in the Electronic Supplementary material and can be visualized in the tooltip window. Coronal sections can be visualized by manipulating the bottom rightcorner panel (labeled A). Specifically, the boxes labeled “C” and “Move with” in the “Clipping” and “Plane” modes in the “Axial” tab must be clicked. The “C” slider can be moved to change levels along the rostro-caudal axis. The numbers indicated in the boxes to the right of the sliders are the distance in mm from the interaural zero line. These numbers are either positive or negative to signify the rostral and caudal positions relative to the zero line, respectively. Sagittal and horizontal sections can be obtained in a similar fashion (click the “S” box for sagittal, or the “H” box for horizontal). 3D image or outlines can be removed or added by clicking the appropriate buttons (labeled 6 and 7). MR images can also be visualized by clicking the appropriate button (labeled 8). Coordinate transformations can be performed in the “Free” tab in the bottom right control panel (labeled A). These transformations can be performed on any combination of Nissl sections, MRI planes, and outlines by clicking the appropriate buttons (labeled 2, 6, 7, and 8) and for any plane of sections by clicking the appropriate buttons (the C, S, and H buttons). The hierarchical organization of the brain structures is indicated in the middle right panel (labeled B). Representative structures are indicated with unique colors in the image
Mentions: The newly developed “SG-eye” software was used for 3D volume rendering of two-dimensional (2D) data (Fiatlux, Tokyo, Japan). SG-eye constructs 3D models by surface rendering and GPU accelerated volume ray-casting. The volume ray-casting algorithm consists of four steps: ray-casting, sampling, shading, and compositing. In the ray-casting step, a ray of sight is cast through the entire volume for each pixel. SG-eye contains several additional functions including position-adjusting, editing of mask images, and labeling and annotating brain regions. The SG-eye operating guide is explained in Fig. 5.

Bottom Line: Degus (Octodon degus) are rodents that are becoming more widely used in the neuroscience field.However, relatively little information is known about the anatomy of degu brains.This manuscript describes the construction of a three-dimensional (3D) volume rendered model of the degu brain that combines histological and magnetic resonance images.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Symbolic Cognitive Development, RIKEN, Brain Science Institute, Wako, Saitama, 351-0198, Japan, nkuma@brain.riken.jp.

ABSTRACT
Degus (Octodon degus) are rodents that are becoming more widely used in the neuroscience field. Degus display several more complex behaviors than rats and mice, including complicated social behaviors, vocal communications, and tool usage with superb manual dexterity. However, relatively little information is known about the anatomy of degu brains. Therefore, for these complex behaviors to be correlated with specific brain regions, a contemporary atlas of the degu brain is required. This manuscript describes the construction of a three-dimensional (3D) volume rendered model of the degu brain that combines histological and magnetic resonance images. This atlas provides several advantages, including the ability to visualize the surface of the brain from any angle. The atlas also permits virtual cutting of brain sections in any plane and provides stereotaxic coordinates for all sections, to be beneficial for both experimental surgeries and radiological studies. The reconstructed 3D atlas is freely available online at: http://brainatlas.brain.riken.jp/degu/modules/xoonips/listitem.php?index_id=24 .

Show MeSH
Related in: MedlinePlus