BrainMaps

Last updated
BrainMaps
BrainMaps treewidget.jpg
Content
DescriptionInteractive zoomable high-resolution digital brain atlas
Data types
captured
Neuroanatomy, Histology
Organisms includes: Man, monkey, cat, mouse, opossum, goldfish, platypus, dog, owl, chicken, rat, and more
Access
Website http://brainmaps.org/
Miscellaneous
License All image dataset is copyrighted to their respective owners, if none indicated, to the UC Regents Davis campus. [1]
Nissl stained, Chlorocebus aethiops brain at BrainMaps.org.
a: choosing from some hundreds of coronal sections.
b: certain coronal section shown.
c: zooming up of insular cortex region.
d: further zooming up of insular cortex. Nissl stained neurons are visible. This slice can be accessed through this link. BrainMap screenshot.jpg
Nissl stained, Chlorocebus aethiops brain at BrainMaps.org.
a: choosing from some hundreds of coronal sections.
b: certain coronal section shown.
c: zooming up of insular cortex region.
d: further zooming up of insular cortex. Nissl stained neurons are visible. This slice can be accessed through this link.

BrainMaps is an NIH-funded interactive zoomable high-resolution digital brain atlas and virtual microscope that is based on more than 140 million megapixels (140 terabytes) of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.

Contents

Currently featured are complete brain atlas datasets for 16 species; a few of which are: Macaca mulatta , Chlorocebus aethiops , Felis silvestris catus , Mus musculus , Rattus norvegicus , and Tyto alba .

The project's principal investigator was UC Davis neuroscientist Ted Jones from 2005 through 2011, after which the role was taken by W. Martin Usrey.

Description

BrainMaps uses multiresolution image formats for representing massive brain images, and a dHTML/Javascript front-end user interface for image navigation, both similar to the way that Google Maps works for geospatial data.

BrainMaps is one of the most massive online neuroscience databases and image repositories and features the highest-resolution whole brain atlas ever constructed. [2] [3]

Extensions to interactive 3-dimensional visualization have been developed through OpenGL-based desktop applications. [4] Freely available image analysis tools enable end-users to datamine online images at the sub-neuronal level. BrainMaps has been used in both research [5] [6] and didactic settings.

Additional images

See also

Related Research Articles

Neuroscience and intelligence refers to the various neurological factors that are partly responsible for the variation of intelligence within species or between different species. A large amount of research in this area has been focused on the neural basis of human intelligence. Historic approaches to studying the neuroscience of intelligence consisted of correlating external head parameters, for example head circumference, to intelligence. Post-mortem measures of brain weight and brain volume have also been used. More recent methodologies focus on examining correlates of intelligence within the living brain using techniques such as magnetic resonance imaging (MRI), functional MRI (fMRI), electroencephalography (EEG), positron emission tomography and other non-invasive measures of brain structure and activity.

<span class="mw-page-title-main">Functional near-infrared spectroscopy</span> Optical technique for monitoring brain activity

Functional near-infrared spectroscopy (fNIRS) is an optical brain monitoring technique which uses near-infrared spectroscopy for the purpose of functional neuroimaging. Using fNIRS, brain activity is measured by using near-infrared light to estimate cortical hemodynamic activity which occur in response to neural activity. Alongside EEG, fNIRS is one of the most common non-invasive neuroimaging techniques which can be used in portable contexts. The signal is often compared with the BOLD signal measured by fMRI and is capable of measuring changes both in oxy- and deoxyhemoglobin concentration, but can only measure from regions near the cortical surface. fNIRS may also be referred to as Optical Topography (OT) and is sometimes referred to simply as NIRS.

Brain mapping is a set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the brain resulting in maps.

<span class="mw-page-title-main">Talairach coordinates</span>

Talairach coordinates, also known as Talairach space, is a 3-dimensional coordinate system of the human brain, which is used to map the location of brain structures independent from individual differences in the size and overall shape of the brain. It is still common to use Talairach coordinates in functional brain imaging studies and to target transcranial stimulation of brain regions. However, alternative methods such as the MNI Coordinate System have largely replaced Talairach for stereotaxy and other procedures.

<span class="mw-page-title-main">Virtual microscopy</span>

Virtual microscopy is a method of posting microscope images on, and transmitting them over, computer networks. This allows independent viewing of images by large numbers of people in diverse locations. It involves a synthesis of microscopy technologies and digital technologies. The use of virtual microscopes can transform traditional teaching methods by removing the reliance on physical space, equipment, and specimens to a model that is solely dependent upon computer-internet access. This increases the convenience of accessing the slide sets and making the slides available to a broader audience. Digitized slides can have a high resolution and are resistant to being damaged or broken over time.

<span class="mw-page-title-main">Christopher deCharms</span>

Dr. Christopher deCharms is a neuroscientist, author, and inventor. Currently, Dr. deCharms is the founder and CEO of Brainful, a life-sciences companies focused on neurotechnology, including technology based on imaging methods that allow people to watch the activation of their own brains 'live' using functional magnetic resonance imaging (fMRI).

<span class="mw-page-title-main">Connectome</span> Comprehensive map of neural connections in the brain

A connectome is a comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram". An organism's nervous system is made up of neurons which communicate through synapses. A connectome is constructed by tracing the neuron in a nervous system and mapping where neurons are connected through synapses.

Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system. More generally, it can be thought of as the study of neuronal wiring diagrams with a focus on how structural connectivity, individual synapses, cellular morphology, and cellular ultrastructure contribute to the make up of a network. The nervous system is a network made of billions of connections and these connections are responsible for our thoughts, emotions, actions, memories, function and dysfunction. Therefore, the study of connectomics aims to advance our understanding of mental health and cognition by understanding how cells in the nervous system are connected and communicate. Because these structures are extremely complex, methods within this field use a high-throughput application of functional and structural neural imaging, most commonly magnetic resonance imaging (MRI), electron microscopy, and histological techniques in order to increase the speed, efficiency, and resolution of these nervous system maps. To date, tens of large scale datasets have been collected spanning the nervous system including the various areas of cortex, cerebellum, the retina, the peripheral nervous system and neuromuscular junctions.

In neuroscience, anterograde tracing is a research method that is used to trace axonal projections from their source to their point of termination. A hallmark of anterograde tracing is the labeling of the presynaptic and the postsynaptic neuron(s). The crossing of the synaptic cleft is a vital difference between the anterograde tracers and the dye fillers used for morphological reconstruction. The complementary technique is retrograde tracing, which is used to trace neural connections from their termination to their source. Both the anterograde and retrograde tracing techniques are based on the visualization of the biological process of axonal transport.

Brain morphometry is a subfield of both morphometry and the brain sciences, concerned with the measurement of brain structures and changes thereof during development, aging, learning, disease and evolution. Since autopsy-like dissection is generally impossible on living brains, brain morphometry starts with noninvasive neuroimaging data, typically obtained from magnetic resonance imaging (MRI). These data are born digital, which allows researchers to analyze the brain images further by using advanced mathematical and statistical methods such as shape quantification or multivariate analysis. This allows researchers to quantify anatomical features of the brain in terms of shape, mass, volume, and to derive more specific information, such as the encephalization quotient, grey matter density and white matter connectivity, gyrification, cortical thickness, or the amount of cerebrospinal fluid. These variables can then be mapped within the brain volume or on the brain surface, providing a convenient way to assess their pattern and extent over time, across individuals or even between different biological species. The field is rapidly evolving along with neuroimaging techniques—which deliver the underlying data—but also develops in part independently from them, as part of the emerging field of neuroinformatics, which is concerned with developing and adapting algorithms to analyze those data.

The Human Connectome Project (HCP) is a five-year project sponsored by sixteen components of the National Institutes of Health, split between two consortia of research institutions. The project was launched in July 2009 as the first of three Grand Challenges of the NIH's Blueprint for Neuroscience Research. On September 15, 2010, the NIH announced that it would award two grants: $30 million over five years to a consortium led by Washington University in St. Louis and the University of Minnesota, with strong contributions from University of Oxford (FMRIB) and $8.5 million over three years to a consortium led by Harvard University, Massachusetts General Hospital and the University of California Los Angeles.

Medical image computing (MIC) is an interdisciplinary field at the intersection of computer science, information engineering, electrical engineering, physics, mathematics and medicine. This field develops computational and mathematical methods for solving problems pertaining to medical images and their use for biomedical research and clinical care.

<span class="mw-page-title-main">Amira (software)</span> Software platform for 3D and 4D data visualization

Amira is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.

A brain atlas is composed of serial sections along different anatomical planes of the healthy or diseased developing or adult animal or human brain where each relevant brain structure is assigned a number of coordinates to define its outline or volume. Brain atlases are contiguous, comprehensive results of visual brain mapping and may include anatomical, genetic or functional features. A functional brain atlas is made up of regions of interest, where these regions are typically defined as spatially contiguous and functionally coherent patches of gray matter.

Vaa3D is an Open Source visualization and analysis software suite created mainly by Hanchuan Peng and his team at Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects. This software has been used in several large neuroscience initiatives and a number of applications in other domains. In a recent Nature Methods review article, it has been viewed as one of the leading open-source software suites in the related research fields. In addition, research using this software was awarded the 2012 Cozzarelli Prize from the National Academy of Sciences.

<span class="mw-page-title-main">Russell Poldrack</span>

Russell "Russ" Alan Poldrack is an American psychologist and neuroscientist. He is a professor of psychology at Stanford University, associate director of Stanford Data Science, member of the Stanford Neuroscience Institute and director of the Stanford Center for Reproducible Neuroscience and the SDS Center for Open and Reproducible Science.

Social cognitive neuroscience is the scientific study of the biological processes underpinning social cognition. Specifically, it uses the tools of neuroscience to study "the mental mechanisms that create, frame, regulate, and respond to our experience of the social world". Social cognitive neuroscience uses the epistemological foundations of cognitive neuroscience, and is closely related to social neuroscience. Social cognitive neuroscience employs human neuroimaging, typically using functional magnetic resonance imaging (fMRI). Human brain stimulation techniques such as transcranial magnetic stimulation and transcranial direct-current stimulation are also used. In nonhuman animals, direct electrophysiological recordings and electrical stimulation of single cells and neuronal populations are utilized for investigating lower-level social cognitive processes.

<span class="mw-page-title-main">Mouse brain</span> Body part used for neuroscience research

The mouse brain refers to the brain of Mus musculus. Various brain atlases exist.

<span class="mw-page-title-main">NeuroVault</span>

NeuroVault is an open-science neuroinformatics online repository of brain statistical maps atlases and parcellations.

References

  1. Terms of Use, BrainMaps.org Access date: 2014-02-11
  2. Mikula, S; Trotts I; Stone JM; Jones EG (2007). "Internet-Enabled High-Resolution Brain Mapping and Virtual Microscopy". NeuroImage. 35 (1): 9–15. doi:10.1016/j.neuroimage.2006.11.053. PMC   1890021 . PMID   17229579.
  3. Mikula, S; Stone JM; Jones EG (2008). "BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy". Brains Minds Media. 3: bmm1426. PMC   2614326 . PMID   19129928.
  4. Trotts, I; Mikula S; Jones EG (2007). "Interactive Visualization of Multiresolution Image Stacks in 3D". NeuroImage. 35 (3): 1038–43. doi:10.1016/j.neuroimage.2007.01.013. PMC   2492583 . PMID   17336095.
  5. Mikula, S; Manger PR; Jones EG (2007). "The thalamus of the monotremes: cyto- and myeloarchitecture and chemical neuroanatomy". Philos Trans R Soc Lond B Biol Sci. 363 (1502): 2415–40. doi:10.1098/rstb.2007.2133. PMC   2606803 . PMID   17553780.
  6. Mikula, S; Parrish SK; Trimmer JS; Jones EG (2009). "Complete 3-D visualization of primate striosomes by KChIP1 immunostaining". J Comp Neurol. 514 (5): 507–17. doi:10.1002/cne.22051. PMC   2737266 . PMID   19350670.