List of neuroscience databases

Last updated

A number of online neuroscience databases are available which provide information regarding gene expression, neurons, macroscopic brain structure, and neurological or psychiatric disorders. Some databases contain descriptive and numerical data, some to brain function, others offer access to 'raw' imaging data, such as postmortem brain sections or 3D MRI and fMRI images. Some focus on the human brain, others on non-human.

Contents

As the number of databases that seek to disseminate information about the structure, development and function of the brain has grown, so has the need to collate these resources themselves. As a result, there now exist databases of neuroscience databases, some of which reach over 3000 entries. [1]

Neuroscience databases


NameDescriptionOrganismLevel (gene, neuron, macroscopic)Data (MRI, fMRI, images, descriptive, numerical)DisorderRegister to view data?Ref.
A Virtual Library for Behavioral Performance in Standard Conditions – Rodent Spontaneous Activity in an Open Field during Repeated Testing and after Treatment with Drugs or Brain LesionsResearch using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test.RatMacroscopicVideoObsessive-compulsive disorderNo [2]
Allen Brain Atlas Atlas, stained sections from brains showing development and gene expressionMouse, HumanMacroscopic, GeneImagesHealthyNo [3]
Alzheimer's Disease Neuroimaging Initiative (ADNI)Structural MRI imagesHumanMacroscopicMRI datasetsHealthy and Alzheimer's disease Yes [4]
Big Brain3D reconstruction of complete brain from cell-body stained histology sections at 20 micron isotropic resolutionHumanMicroscopicImagesHealthyNo [5]
BIRN fMRI and MRI datafMRI, MRI scans and atlases for human and mouse brainsMouse, HumanMultilevel: brain regions, connections, neurons, gene expression patternsMRI datasets, fMRI datasetsHealthy, Elderly No
Bipolar Disorder Neuroimaging DatabaseMeta-analysis and database of MRI studiesHumanMacroscopicDescriptive, numerical Bipolar Disorder No [6]
Brain Architecture Management SystemOnline resource for information about neural circuitryRat, mouse, humanMultilevel: brain regions, connections, neurons, gene expression patternsDescriptive, numericalHealthyNo
Brain CloudGene expression in the human prefrontal cortexHumanGene expression patternsDescriptive, numericalHealthyNo
Brain-CODE A multi-modal, cross-disorder platform for integrated neuroscience research and data by the Ontario Brain Institute.Human, AnimalMultimodal datasets (clinical, imaging, molecular, etc.)Descriptive, numerical, imaging, molecular, geneticsNeurodevelopmental, Cerebral Palsy, Epilepsy, Depression, Neurodegeneration, ConcussionYes [7]
Brain-Development.orgStructural MRI images and AtlasesHumanMacroscopicMRI datasetsFetuses, healthy and prematurely born neonatesYes [8]
Braingraph.orgBraingraphs computed from the Human Connectome Project dataHumanMacroscopic, up to 1015 nodesdirected and undirected graphs in anatomically annotated GraphML formatHealthyNo [9]
BraininfoAtlas, schematic atlas of Macaca fascicularis Macaque MacroscopicSchematic imagesHealthyYes
Brain Machine Interface PlatformDifferent types of data related to brain machine interfaceHuman, MonkeyMacroscopic, NeuronImages, NumericalHealthyNo
BrainMap.orgfMRI coordinate databaseHumanMacroscopicDescriptiveHealthyYes [10]
BrainMaps Atlas, high resolution stained sections from brainsHuman, primate and non-primate (14 species in all)Neuron and MacroscopicImagesHealthyNo [11]
Brain/MINDS Dataportal Atlas, in-vivo and ex-vivo MRI scans, ECoG recordingsCommon Marmoset, HumanMacroscopicImagesHealthyNo [12]
Brede DatabasefMRI and PET coordinate databaseHumanMacroscopicDescriptiveHealthyNo [13]
Brainmuseum.org / MSU Brain Biodiversity BankAtlas, stained sections from brains and MRI imagesHuman and 62 other speciesMacroscopicImagesHealthyNo
Brainomics/LocalizerfMRI and MRI scans, behavioral dataHumanMacroscopicImages, NumericalHealthyNo [14]
BuzLabDB: The Buzsaki Lab Databank Electrophysiological recordings performed in freely moving rats and mice collected by investigators in the Buzsaki LabMice and ratsMultiscaleSpike trains, LFP, Raw ephys dataHealthyNo [15] [16]
Caltech Subcortical AtlasMRI scansHumanMacroscopicMRIHealthyNo [17]
Cambridge Centre for Ageing and Neuroscience (Cam-CAN)MRI, fMRI, MEG data for ~700 population-derived healthy adults aged 18–88HumanMacroscopicImages, Descriptive, NumericalHealthyNo [18]
The Cancer Imaging ArchiveMRI, CT, and PET imaging of cancer patients with supporting clinical data (in many cases)HumanMacroscopicImages, Descriptive, NumericalCancerNo [19]
Cerebellar Development Transcriptome DatabaseAtlas, stained sections from mouse brains showing cerebellar development and gene expressionMouseMacroscopic, GeneImagesHealthyNo [20]
Collaborative Research in Computational Neuroscience (CRCNS.org)Many kinds of neuroscience results that are relevant for modelingHuman and several other speciesMultiscaleSpike trains, LFP, MUA, MRIHealthyYes
DANDI: Distributed Archives for Neurophysiology Data Integration cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experimentsHuman and several other speciesMultiscaleSpike trains, LFP, MUA, MRIHealthy
Database for Reaching Experiments And Models (DREAM)Reaching data (behavioral, generalization, adaptation, learning, spike, fMRI, uncertainty)Human and monkeyMacroscopicKinematic, Spike, fMRIHealthyYes
The fMRI Data Center fMRI datasets from published studiesHumanMacroscopicfMRI datasetsHealthyYes [21]
GLIMPS Project (GLucose IMaging in Parkinsonian Syndromes)International FDG-PET scan neurodegenerative disease databaseHumanMacroscopic FDG-PET images Parkinson's disease (PD), Alzheimer's disease (AD), multiple system atrophy (MSA), progressive supranuclear palsy (PSP), etc.Yes
Hippocampome PortalCircuitry, neural types, electrophysiologyAdult humanNeuronCell morphology, electrophysiology, region makeup, connectivityHealthyYes [22] [23]
IBA: Infant Brain Atlas Infant brain atlases from 2 weeks to 2 years of ageHuman infantsMacroscopic, microscopic, brain regionsMRIHealthyNo [24]
International Epilepsy Electrophysiology Database (IEEG.org)EEG, metadata, imaging, annotations on dataHumans and animal models of epilepsyEEG, local fields, micro-ECoGElectrophysiologyNon-healthy, several healthyYes
International Neuroimaging Data-sharing Initiative (INDI)Functional connectivity data from many different groupsInvertebrates (47 species in all)MacroscopicFunctional connectivityHealthy, non-healthyYes
Invertebrate Brain PlatformPhotos of dissections of invertebrates nervous systemsInvertebrates (47 species in all)MacroscopicPhotosHealthyNo
In vivo human phantomUltrahigh resolution MRI data of a single participant including 150 μm ToF angiography, 250 μm T1-weighted MPRAGE, 330 μm QSM, 450 μm T2-weighted TSE, 800 μm DTI, one hour continuous 1.8 mm rs-fMRI and structural data acquired over more than a decadeHumanMesoscopicStructural MRI with various contrasts, microstructure MRI and functional MRIHealthyNo [25]
JuBrain atlasProbabilistic cytoarchitectonic 3D maps of the human brainHumanMesoscopicStructuralHealthyNo [26] [27]
Kymata AtlasFunctional atlas of the human cortexHumanMacroscopicFunctionalHealthyNo [28]
Major Depressive Disorder Neuroimaging DatabaseMeta-analysis and database of MRI studiesHumanMacroscopicDescriptive, numerical Major Depressive Disorder No [29]
Marmoset Gene Atlas Gene expression in the common marmoset whole brainCommon MarmosetMacroscopic, GeneImagesHealthyNo [30]
Mouse Brain LibraryAtlas, stained sections from mouse brainsMouseMacroscopicImagesHealthyNo [31]
MouseLight Complete, whole-brain reconstructionsMouseNeuronCell morphology, projectome connectivityHealthyNo [32]
NeuroData Volumetric datasets, atlases, and connectomics researchMultipleMultiscaleImages (3D, 4D)VariousNo
Neuroelectro.orgElectrophysiology of neuronsHuman, othersNeuronElectrophysiological properties and dataHealthyNo [33]
Neuromorpho.org3D models of real neuronsHuman, rat, mouse, monkey, othersNeuronImages and 3D dataHealthyNo [34]
Neuromorphometrics.com Manually labeled MRI Brain ScansHumanMacroscopicT1-weighted MRI, labeled volumesHealthyNo
NeuronDBDatabase of Neuron properties and classificationHumanNeuronDescriptiveHealthyNo [35]
Neuroimaging Tools and Resources Collaboratory (NITRC) Award-winning free collaboratory with over 1000 neuroinformatics software tools, imaging datasets, and community resources including forums and events.Human, mouse, rat, otherMicroscopic, macroscopicDatasetsHealthy and diseased No
Open Access Series of Imaging Studies (OASIS)Structural MRI imagesHumanMacroscopicMRI datasetsHealthy and Alzheimer's disease Yes [36]
Open Connectome ProjectDatabase of different circuitry frameworks and neuroimaging datasets, including volumetric datasets, atlases, and connectomics researchHuman, mouse, bat, zebrafish, insect, otherMultilevel: brain regions, connections, neurons, gene expression patternsImages and 3D dataHealthyNo [37]
openfnirs a meta-database specific to fNIRS data. The “Openfnirs meta-database” (https://openfnirs.org/data/) is a part of the openfnirs initiative whose mission is to foster the development of an fNIRS ecosystem and to promote the open dissemination of fNIRS hardware and software, as well as provide access to resources, documentation and training opportunities for fNIRS users.HumanMacroscopicfNIRS (Functional_near-infrared_spectroscopy)Healthy and eventually various diseasesNo [38]
OpenNeuro Large and diverse collection of raw data from various research studies distributed under permissive licenses (CC0 and CC BY). All datasets are formatted according to the same format (Brain Imaging Data Structure) and can be accessed via Amazon S3.HumanMacroscopicFunctional, structural, diffusion MRI, and Magnetoencephalography datasetsHealthy and various diseasesNo [39]
Open MEG Archive (OMEGA) Magnetoencephalography, structural MRI datasets, and demographicsHumanMacroscopicMEG, T1 MRI datasets, demographic dataHealthy, ADHD, Traumatic brain injury Yes [40]
The PAIN RepositoryStructural, Diffusion and Functional MRI datasetsHumanHuman MacroscopicMRI datasets and MetadataHealthy and Pain ConditionsYes [41]
Pig Brain AtlasPig Brain Atlas is a three-dimensional MRI-based averaged brain and atlas of the neonatal piglet (Sus scrofa).Pig (Sus scrofa)MacroscopicStructural MRIHealthyYes [42]
Primate Cell Type Database PrimateDatabase.com, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology.Non-human primate and humanNeuronElectrophysiology, Morphology and 3-d ReconstructionsHealthyNo
SchizConnectSchizConnect is an open, public search-and-download virtual database for schizophrenia neuroimaging (MRI) images and related data.HumanMacroscopicStructural, Diffusion and Functional MRI datasets, cognitive and clinical assessmentsSchizophrenia (+ siblings), Bipolar Disorder, Controls (+ siblings)Yes [43]
Temple EEG DatabaseOver 30,000 clinical EEGs and accompanying neurologist reportsHumanMacroscopicEEGHealthy and various diseasesYes [44]
Ultrahigh resolution T1-weighted whole brain MR datasetT1-weighted MR data acquired using prospective motion correction at an ultrahigh isotropic resolution of 250 µm.HumanMesoscopicStructural MRI dataset including scanner's raw to processed dataHealthyNo [45]
UNC-Wisconsin Neurodevelopment Rhesus MRI DatabaseStructural and Diffusion Weighted MRI images in Native and Atlas Space Macaque MacroscopicMRI datasetsHealthyNo
Whole Brain AtlasAtlas, Structural MRI images and PET imagesHumanMacroscopicImagesHealthy and various diseasesNo
NeuroVault Unthresholded statistical maps from MRI and PET studies.HumanMacroscopicImagesHealthy and various diseasesNo [46]

Databases of neuroscience databases

NameDescriptionOrganismLevel (gene, neuron, macroscopic)Data (MRI, fMRI, images, descriptive, numerical)DisorderRegister to view data?Ref.
Neuroscience Information Framework A meta database of neuroscience-relevant data incorporating over 100 databases.Human, mouse, rat, wormMicroscopic, macroscopicDatasetsHealthy and diseased No [47]

Neuroscience article aggregators

Neuroscience feed at RightRelevance. [48]

See also

Related Research Articles

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">FreeSurfer</span> Brain imaging software package

FreeSurfer is a brain imaging software package originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve. Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer contains a set of programs with a common focus of analyzing magnetic resonance imaging (MRI) scans of brain tissue. It is an important tool in functional brain mapping and contains tools to conduct both volume based and surface based analysis. FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and pial surfaces, for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds.

<span class="mw-page-title-main">International Neuroinformatics Coordinating Facility</span>

The International Neuroinformatics Coordinating Facility is an international non-profit organization with the mission to develop, evaluate, and endorse standards and best practices that embrace the principles of Open, FAIR, and Citable neuroscience. INCF also provides training on how standards and best practices facilitate reproducibility and enables the publishing of the entirety of research output, including data and code. INCF was established in 2005 by recommendations of the Global Science Forum working group of the OECD. The INCF is hosted by the Karolinska Institutet in Stockholm, Sweden. The INCF network comprises institutions, organizations, companies, and individuals active in neuroinformatics, neuroscience, data science, technology, and science policy and publishing. The Network is organized in governing bodies and working groups which coordinate various categories of global neuroinformatics activities that guide and oversee the development and endorsement of standards and best practices, as well as provide training on how standards and best practices facilitate reproducibility and enables the publishing of the entirety of research output, including data and code. The current Directors are Mathew Abrams and Helena Ledmyr, and the Governing Board Chair is Maryann Martone

<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.

<span class="mw-page-title-main">Default mode network</span> Large-scale brain network active when not focusing on an external task

In neuroscience, the default mode network (DMN), also known as the default network, default state network, or anatomically the medial frontoparietal network (M-FPN), is a large-scale brain network primarily composed of the dorsal medial prefrontal cortex, posterior cingulate cortex, precuneus and angular gyrus. It is best known for being active when a person is not focused on the outside world and the brain is at wakeful rest, such as during daydreaming and mind-wandering. It can also be active during detailed thoughts related to external task performance. Other times that the DMN is active include when the individual is thinking about others, thinking about themselves, remembering the past, and planning for the future.

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.

Anders Martin Dale is a prominent neuroscientist and professor of radiology, neurosciences, psychiatry, and cognitive science at the University of California, San Diego (UCSD), and is one of the world's leading developers of sophisticated computational neuroimaging techniques. He is the founding Director of the Center for Multimodal Imaging Genetics (CMIG) at UCSD.

<span class="mw-page-title-main">Resting state fMRI</span> Type of functional magnetic resonance imaging

Resting state fMRI is a method of functional magnetic resonance imaging (fMRI) that is used in brain mapping to evaluate regional interactions that occur in a resting or task-negative state, when an explicit task is not being performed. A number of resting-state brain networks have been identified, one of which is the default mode network. These brain networks are observed through changes in blood flow in the brain which creates what is referred to as a blood-oxygen-level dependent (BOLD) signal that can be measured using fMRI.

Connectograms are graphical representations of connectomics, the field of study dedicated to mapping and interpreting all of the white matter fiber connections in the human brain. These circular graphs based on diffusion MRI data utilize graph theory to demonstrate the white matter connections and cortical characteristics for single structures, single subjects, or populations.

Dynamic functional connectivity (DFC) refers to the observed phenomenon that functional connectivity changes over a short time. Dynamic functional connectivity is a recent expansion on traditional functional connectivity analysis which typically assumes that functional networks are static in time. DFC is related to a variety of different neurological disorders, and has been suggested to be a more accurate representation of functional brain networks. The primary tool for analyzing DFC is fMRI, but DFC has also been observed with several other mediums. DFC is a recent development within the field of functional neuroimaging whose discovery was motivated by the observation of temporal variability in the rising field of steady state connectivity research.

<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.

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

OpenNeuro is an open-science neuroinformatics database storing datasets from human brain imaging research studies.

Viktor K. Jirsa is a German physicist and neuroscientist, director of research at the Centre national de la recherche scientifique (CNRS), director of the Institut de Neuroscience des Systèmes and co-director of the Fédération Hospitalo-Universitaire (FHU) EPINEXT "Epilepsy and Disorders of Neuronal Excitability" in Marseille, France. He is workpackage leader in the Epinov project funded in the context of the RHU3 call and coordinated by Fabrice Bartolomei.

<span class="mw-page-title-main">John-Dylan Haynes</span> British-German brain researcher (born 1971)

John-Dylan Haynes is a British-German brain researcher.

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">NeuroVault</span>

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

Network neuroscience is an approach to understanding the structure and function of the human brain through an approach of network science, through the paradigm of graph theory. A network is a connection of many brain regions that interact with each other to give rise to a particular function. Network Neuroscience is a broad field that studies the brain in an integrative way by recording, analyzing, and mapping the brain in various ways. The field studies the brain at multiple scales of analysis to ultimately explain brain systems, behavior, and dysfunction of behavior in psychiatric and neurological diseases. Network neuroscience provides an important theoretical base for understanding neurobiological systems at multiple scales of analysis.

<span class="mw-page-title-main">Dimitri Van De Ville</span> Swiss-Belgian computer scientist and neuroscientist specialized in brain activity networks

Dimitri Van De Ville is a Swiss and Belgian computer scientist and neuroscientist specialized in dynamical and network aspects of brain activity. He is a professor of bioengineering at EPFL and the head of the Medical Image Processing Laboratory at EPFL's School of Engineering.

References

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