BigBrain is a freely accessible high-resolution 3D digital

atlas An atlas is a collection of maps; it is typically a bundle of maps of Earth or of a region of Earth. Atlases have traditionally been bound into book form, but today many atlases are in multimedia formats. In addition to presenting geograp ...

of the

human brain The human brain is the central organ (anatomy), organ of the human nervous system, and with the spinal cord makes up the central nervous system. The brain consists of the cerebrum, the brainstem and the cerebellum. It controls most of the act ...

, released in June 2013 by a team of researchers at the

Montreal Neurological Institute The McGill University Health Centre (MUHC; french: Centre universitaire de santé McGill) is one of two major healthcare networks in the city of Montreal, Quebec. It is affiliated with McGill University and is one of the largest medical complex in ...

and the German

Forschungszentrum Jülich Forschungszentrum Jülich (FZJ here for short) is a national research institution that pursues interdisciplinary research in the fields of energy, information, and bioeconomy. It operates research infrastructures with a focus on supercomputers. C ...

and is part of the European

Human Brain Project The Human Brain Project (HBP) is a large ten-year scientific research project, based on exascale supercomputers, that aims to build a collaborative ICT-based scientific research infrastructure to allow researchers across Europe to advance knowle ...

. The isotropic 3D spatial resolution of the BigBrain atlas is 20

μm The micrometre ( international spelling as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American spelling), also commonly known as a micron, is a unit of length in the International System of Uni ...

, much finer than the typical 1 mm resolution of other existing 3D models of the human brain such as the

Allen Brain Atlas The Allen Mouse and Human Brain Atlases are projects within the Allen Institute for Brain Science which seek to combine genomics with neuroanatomy by creating gene expression maps for the mouse and human brain. They were initiated in September 2 ...

. In 2014, BigBrain was cited in the top 10

MIT Technology Review ''MIT Technology Review'' is a bimonthly magazine wholly owned by the Massachusetts Institute of Technology, and editorially independent of the university. It was founded in 1899 as ''The Technology Review'', and was re-launched without "The" in ...

Acquisition

The atlas was created from the brain of an unidentified 65-year-old man (it was "65-year-old female", according to "BigBrain: An Ultrahigh-Resolution3D Human Brain Model", page 1472, Amunts K et al, SCIENCE, 21 JUNE 2013 VOL 340) who died with no known brain pathology. His brain, after being removed from the skull, was first scanned using an MRI machine, then embedded in

paraffin Paraffin may refer to: Substances * Paraffin wax, a white or colorless soft solid that is used as a lubricant and for other applications * Liquid paraffin (drug), a very highly refined mineral oil used in cosmetics and for medical purposes * Alkane ...

and sliced into 7,404 20 μm thick sections using a large-scale

microtome A microtome (from the Greek ''mikros'', meaning "small", and ''temnein'', meaning "to cut") is a cutting tool used to produce extremely thin slices of material known as ''sections''. Important in science, microtomes are used in microscopy, allow ...

. After each section was removed, the uncut face was photographed in order to provide an additional reference for removing distortion. The brain sections were placed on large glass slides and then

stained A stain is a discoloration that can be clearly distinguished from the surface, material, or medium it is found upon. They are caused by the chemical or physical interaction of two dissimilar materials. Accidental staining may make materials app ...

for cell bodies using the Merker method, a process that causes the

grey matter Grey matter is a major component of the central nervous system, consisting of neuronal Soma (biology), cell bodies, neuropil (dendrites and unmyelinated axons), Glia, glial cells (astrocytes and oligodendrocytes), synapses, and Capillary, capil ...

in the brain to be darkly stained while leaving the

white matter White matter refers to areas of the central nervous system (CNS) that are mainly made up of myelinated axons, also called tracts. Long thought to be passive tissue, white matter affects learning and brain functions, modulating the distributi ...

uncoloured. The stained sections were scanned and digitized using a

flatbed scanner An image scanner—often abbreviated to just scanner—is a device that optically scans images, printed text, handwriting or an object and converts it to a digital image. Commonly used in offices are variations of the desktop ''flatbed scanner'' w ...

at 2400dpi, creating a one terabyte raw record. The acquisition process took about 1,000 hours of labor.

Image processing

The resulting digital images were then processed by human operators to remove artifacts, and by software to align them with the reference images and with neighbouring sections, thereby correcting distortions that inevitably arise during

histological Histology, also known as microscopic anatomy or microanatomy, is the branch of biology which studies the microscopic anatomy of biological tissues. Histology is the microscopic counterpart to gross anatomy, which looks at larger structures vis ...

processing. The corrected data were then assembled into a three-dimensional computer model with a spatial isotropic 3D resolution of 20 μm. The atlas took five years to complete.Healy, Melissa. (2013, June 20) 'Scientists create detailed 3D model of human brain,' ''Los Angeles Times'' http://articles.latimes.com/2013/jun/20/science/la-sci-big-brain-20130621 Retrieved 19 Oct 2013. The database for the atlas is accessible on the web a
bigbrainproject.org
Announced plans include mapping additional brains and providing tools to allow brain scans from medical patients to be aligned to the BigBrain structure.

Notes and references

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External links

BigBrain data files made available at the MNIYouTube demo
Computational neuroscience Scientific databases Neuroanatomy

Acquisition

Image processing

See also

Notes and references

External links