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Resource:Human Brain Atlas

Name: Resource:Human Brain Atlas
Description: In this atlas you can view MRI sections through a living human brain as well as corresponding sections stained for cell bodies or for nerve fibers. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies.

For the stained sections, the brain was removed from the skull, dehydrated, embedded in celloidin, cut with a sliding microtome, passed through several staining and differentiating solutions, and mounted on glass slides. Each step of these procedures changed the shaped of the brain and of the sections. Therefore the stained sections will be quite a different size and shape than those of the MRI sections. Nevertheless, comparing MRI images with stained sections from approximately the same level can greatly increase understanding of the internal architecture of these brains.

Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process.

We here present an electronic anatomically labeled three-dimensional atlas of the human brain created from MRI images. In conjunction we present anatomically labeled stained sections that correspond to the three-dimensional MRI images. In this way we utilize the advantages of both methods.

MATERIALS AND METHODS
MRI Specimen
The MRI subject was a 22-year-old adult male weighing 79kg with a body length of 1.87m.

Magnetic Resonance Imaging
The imaging was performed on a 1.5 Tesla LX Cardiovascular Magnetic Resonance (CVMR) system (General Electric Co., Waukesha, WI). This system is equipped with 40 milliTesla gradients with a slew rate of 150 Tesla/meter/second. The subject was placed in the magnet in the supine position with his head firmly fixed via a bite bar in a standard quadrature birdcage head coil. The subject was scanned using a 3D fast Spoiled Grass (Fast SPGR) sequence, TR 50 ms, TE 2.4 ms, FOV 24 cm, slice thickness 1.5 mm was acquired. The scan covered the entire extent of the brain in the inferior/superior direction.

Three-Dimensional Reconstruction and Reformatting
Computer-generated 3D reconstruction images were created from MRI scans in the axial (horizontal) plane, using the software programs VoxelView and VoxelMath programs (Vital Images, Inc.) at the Laser Scanning Microscopy Laboratory at Michigan State University, Dr. Joanne Whallon, Director. The 3D rendered model, wherein details of internal and external morphology are represented in three-dimensional space, was then digitally resectioned in orthogonal planes to produce corresponding virtual section series in the coronal and sagittal planes.

Stained Sections
The stained sections are from the Yakovlev-Haleem Collection in the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, D. C. Sections in the coronal plane are from specimen STD-IIIA, those in the horizontal plane are from specimen SP-18, and those in the sagittal plane are from specimen VND-31-84.

Anatomical Labeling and Nomenclature

The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp
Other Name(s): Michigan State University Brain Biodiversity Bank - Human Brain Atlas, MSU Brain Biodiversity Bank - Human Brain Atlas
Parent Organization: Michigan State University; Michigan; USA
Supporting Agency: National Science Foundation
Related to: NIF Data Federation
Resource Type(s): Atlas, Video, Training material
Keywords: human, adult, MRI, fiber stain, anatomy, normal, neuroanatomy, nissil stain, cell stain, image, brainstem, cell bodies, nerve fibers, brain, coronal, sagittal, horizontal, fiber, 3D model, montage, screensaver, Weil, hypothalamus
Grant: IBN 0131267, 0131826, 0131028
Abbreviation: Human Brain Atlas
Resource: Resource
URL: https://www.msu.edu/~brains/brains/human/index.html
Id: nif-0000-00088
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Facts about Resource:Human Brain AtlasRDF feed
AbbrevHuman Brain Atlas  +
CurationStatuscurated  +
DefiningCitationhttps://www.msu.edu/~brains/brains/human/index.html  +
DefinitionIn this atlas you can view MRI sections th In this atlas you can view MRI sections through a living human brain as well as corresponding sections stained for cell bodies or for nerve fibers. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies.

For the stained sections, the brain was removed from the skull, dehydrated, embedded in celloidin, cut with a sliding microtome, passed through several staining and differentiating solutions, and mounted on glass slides. Each step of these procedures changed the shaped of the brain and of the sections. Therefore the stained sections will be quite a different size and shape than those of the MRI sections. Nevertheless, comparing MRI images with stained sections from approximately the same level can greatly increase understanding of the internal architecture of these brains.

Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process.

We here present an electronic anatomically labeled three-dimensional atlas of the human brain created from MRI images. In conjunction we present anatomically labeled stained sections that correspond to the three-dimensional MRI images. In this way we utilize the advantages of both methods.

MATERIALS AND METHODS
MRI Specimen
The MRI subject was a 22-year-old adult male weighing 79kg with a body length of 1.87m.

Magnetic Resonance Imaging
The imaging was performed on a 1.5 Tesla LX Cardiovascular Magnetic Resonance (CVMR) system (General Electric Co., Waukesha, WI). This system is equipped with 40 milliTesla gradients with a slew rate of 150 Tesla/meter/second. The subject was placed in the magnet in the supine position with his head firmly fixed via a bite bar in a standard quadrature birdcage head coil. The subject was scanned using a 3D fast Spoiled Grass (Fast SPGR) sequence, TR 50 ms, TE 2.4 ms, FOV 24 cm, slice thickness 1.5 mm was acquired. The scan covered the entire extent of the brain in the inferior/superior direction.

Three-Dimensional Reconstruction and Reformatting
Computer-generated 3D reconstruction images were created from MRI scans in the axial (horizontal) plane, using the software programs VoxelView and VoxelMath programs (Vital Images, Inc.) at the Laser Scanning Microscopy Laboratory at Michigan State University, Dr. Joanne Whallon, Director. The 3D rendered model, wherein details of internal and external morphology are represented in three-dimensional space, was then digitally resectioned in orthogonal planes to produce corresponding virtual section series in the coronal and sagittal planes.

Stained Sections
The stained sections are from the Yakovlev-Haleem Collection in the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, D. C. Sections in the coronal plane are from specimen STD-IIIA, those in the horizontal plane are from specimen SP-18, and those in the sagittal plane are from specimen VND-31-84.

Anatomical Labeling and Nomenclature

The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp
ed. Academic Press. San Diego, CA. 256 pp
ExampleImageHuman Brain Atlas.PNG  +
GrantCategory:IBN 0131267   +, Category:0131826   +, and Category:0131028   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleAtlas  +, Video  +, and Training material  +
Idnif-0000-00088  +
Is part ofMichigan State University; Michigan; USA  +
KeywordsHuman  +, Adult  +, MRI  +, Fiber stain  +, Anatomy  +, Normal  +, Neuroanatomy  +, Nissil stain  +, Cell stain  +, Image  +, Brainstem  +, Cell bodies  +, Nerve fibers  +, Brain  +, Coronal  +, Sagittal  +, Horizontal  +, Fiber  +, 3D model  +, Montage  +, Screensaver  +, Weil  +, and Hypothalamus  +
LabelResource:Human Brain Atlas  +
ModifiedDate24 April 2012  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToNIF Data Federation  +
Supporting AgencyNational Science Foundation  +
SynonymMichigan State University Brain Biodiversity Bank - Human Brain Atlas  +, and MSU Brain Biodiversity Bank - Human Brain Atlas  +