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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.

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]

Contents

Neuroscience databasesEdit

Name Description Organism Level (gene, neuron, macroscopic) Data (MRI, fMRI, images, descriptive, numerical) Disorder Register to view data? Ref
Allen Brain Atlas Atlas, stained sections from brains showing development and gene expression Mouse, Human Macroscopic, Gene Images Healthy No [2]
Alzheimer's Disease Neuroimaging Initiative (ADNI) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's Disease Yes [3]
Big Brain 3D reconstruction of complete brain from cell-body stained histology sections at 20 micron isotropic resolution Human Microscopic Images Healthy No [4]
BIRN fMRI and MRI data fMRI, MRI scans and atlases for human and mouse brains Mouse, Human Multilevel: brain regions, connections, neurons, gene expression patterns MRI datasets, fMRI datasets Healthy, Elderly No
Bipolar Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Bipolar Disorder No [5]
Brain Architecture Management System Online resource for information about neural circuitry Rat, Mouse, Human Multilevel: brain regions, connections, neurons, gene expression patterns Descriptive, numerical Healthy No
Brain Cloud Gene expression in the human prefrontal cortex Human Gene expression patterns Descriptive, numerical Healthy No
Brain-Development.org Structural MRI images and Atlases Human Macroscopic MRI datasets Fetuses, healthy and prematurely born neonates Yes [6]
Braingraph.org Braingraphs computed from the Human Connectome Project data Human Macroscopic, up to 1015 nodes directed and undirected graphs in anatomically annotated GraphML format Healthy No [7]
Braininfo Atlas, schematic atlas of Macaca fascicularis Macaque Macroscopic Schematic images Healthy Yes
Brain Machine Interface Platform Different types of data related to brain machine interface Human, Monkey Macroscopic, Neuron Images, Numerical Healthy No
BrainMap.org fMRI coordinate database Human Macroscopic Descriptive Healthy Yes [8]
BrainMaps Atlas, high resolution stained sections from brains Human, primate and non-primate (14 species in all) Neuron and Macroscopic Images Healthy No [9]
Brede Database fMRI and PET coordinate database Human Macroscopic Descriptive Healthy No [10]
Brainmuseum.org / MSU Brain Biodiversity Bank Atlas, stained sections from brains and MRI images Human and 62 other species Macroscopic Images Healthy No
Brainomics/Localizer fMRI and MRI scans, behavioral data Human Macroscopic Images, Numerical Healthy No [11]
Caltech Subcortical Atlas MRI scans Human Macroscopic MRI Healthy No [12]
The Cancer Imaging Archive MRI, CT, and PET imaging of cancer patients with supporting clinical data (in many cases) Human Macroscopic Images, Descriptive, Numerical Cancer No [13]
Cerebellar Development Transcriptome Database Atlas, stained sections from mouse brains showing cerebellar development and gene expression Mouse Macroscopic, Gene Images Healthy No [14]
Collaborative Research in Computational Neuroscience CRCNS.org Many kinds of neuroscience results that are relevant for modeling Human and several other species Multiscale Spike trains, LFP, MUA, MRI Healthy Yes
Database for Reaching Experiments And Models (DREAM) Reaching data. (Behavioral, generalization, adaptation, learning, spike, fMRI, uncertainty) Human and monkey Macroscopic Kinematic, Spike, fMRI Healthy Yes
The fMRI Data Center fMRI datasets from published studies Human Macroscopic fMRI datasets Healthy Yes [15]
GLIMPS Project (GLucose IMaging in Parkinsonian Syndromes) International FDG-PET scan neurodegenerative disease database Human Macroscopic FDG-PET images Parkinson's (PD), Alzheimer's(AD), Multiple System Atrophy (MSA), Progressive Supranuclear Palsy (PSP), etc. Yes
Hippocampome Portal Circuitry, neural types, electrophysiology Adult human Neuron Cell morphology, electrophysiology, region makeup, connectivity Healthy Yes [16][17]
International Epilepsy Electrophysiology Database (IEEG.org) EEG, metadata, imaging, annotations on data Humans and animal models of epilepsy EEG, local fields, micro-ECoG Electrophysiology Non-healthy, several healthy Yes
International Neuroimaging Data-sharing Initiative (INDI) Functional connectivity data from many different groups Invertebrates (47 species in all) Macroscopic Functional connectivity Healthy, non-healthy Yes
Invertebrate Brain Platform Photos of dissections of invertebrates nervous systems Invertebrates (47 species in all) Macroscopic Photos Healthy No
JuBrain atlas Probabilistic cytoarchitectonic 3D maps of the human brain Human Mesoscopic Structural Healthy No [18][19]
Kymata Atlas Functional atlas of the human cortex Human Macroscopic Functional Healthy No [20]
Major Depressive Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Major Depressive Disorder No [21]
Mouse Brain Library Atlas, stained sections from mouse brains Mouse Macroscopic Images Healthy No [22]
NeuroData Volumetric datasets, atlases, and connectomics research Multiple Multiscale Images (3D, 4D) Various No
Neuroelectro.org Electrophysiology of neurons Human, others Neuron Electrophysiological properties and data Healthy No [23]
Neuromorpho.org 3D models of real neurons Human, Rat, Mouse, Monkey, others Neuron Images and 3D data Healthy No [24]
Neuromorphometrics.com Manually labeled MRI Brain Scans Human Macroscopic T1-weighted MRI, labeled volumes Healthy No
NeuronDB Database of Neuron properties and classification Human Neuron Descriptive Healthy No [25]
Open Access Series of Imaging Studies (OASIS) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's Disease Yes [26]
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. Human Macroscopic Functional, structural, diffusion MRI, and Magnetoencephalography datasets Healthy and various dieseses No [27]
Open MEG Archive (OMEGA) Magnetoencephalography, structural MRI datasets, and demographics Human Macroscopic MEG, T1 MRI datasets, demographic data Healthy, ADHD, Traumatic brain injury Yes [28]
The PAIN Repository Structural, Diffusion and Functional MRI datasets Human Human Macroscopic MRI datasets and Metadata Healthy and Pain Conditions Yes [29]
Pig Brain Atlas Pig Brain Atlas is a three-dimensional MRI-based averaged brain and atlas of the neonatal piglet (Sus scrofa). Pig (Sus scrofa) Macroscopic Structural MRI Healthy Yes [30]
SchizConnect SchizConnect is an open, public search-and-download virtual database for schizophrenia neuroimaging (MRI) images and related data. Human Macroscopic Structural, Diffusion and Functional MRI datasets, cognitive and clinical assessments Schizophrenia (+ siblings), Bipolar Disorder, Controls (+ siblings) Yes [31]
Temple EEG Database Over 30,000 clinical EEGs and accompanying neurologist reports Human Macroscopic EEG Healthy and various diseases Yes [32]
Ultrahigh resolution T1-weighted whole brain MR dataset T1-weighted MR data acquired using prospective motion correction at an ultrahigh isotropic resolution of 250 µm. Human Mesoscopic Structural MRI dataset including scanner's raw to processed data Healthy No [33]
UNC-Wisconsin Neurodevelopment Rhesus MRI Database Structural and Diffusion Weighted MRI images in Native and Atlas Space Macaque Macroscopic MRI datasets Healthy No
Whole Brain Atlas Atlas, Structural MRI images and PET images Human Macroscopic Images Healthy and various diseases No
NeuroVault Unthresholded statistical maps from MRI and PET studies. Human Macroscopic Images Healthy and various diseases No [34]

Databases of Neuroscience databasesEdit

Name Description Organism Level (gene, neuron, macroscopic) Data (MRI, fMRI, images, descriptive, numerical) Disorder Register to view data? Ref
Neuroscience Information Framework A meta database of neuroscience-relevant data incorporating over 100 databases. Human, Mouse, Rat, Worm Microscopic, Macroscopic Datasets Healthy and Diseased No [35]
Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) NITRC facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses. Human, Mouse, Rat, Worm Microscopic, Macroscopic Datasets Healthy and Diseased No

Neuroscience article aggregatorsEdit

Neuroscience feed at RightRelevance.[36]

See alsoEdit

ReferencesEdit

  1. ^ "Number of entries using search query 'database'". neuinfo.org. NIF. Retrieved 25 Jan 2015.
  2. ^ Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, et al. (January 2007). "Genome-wide atlas of gene expression in the adult mouse brain". Nature. 445 (7124): 168–76. Bibcode:2007Natur.445..168L. doi:10.1038/nature05453. PMID 17151600.
  3. ^ Jack CR, Bernstein MA, Fox NC, Thompson P, Alexander G, Harvey D, et al. (April 2008). "The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods". Journal of Magnetic Resonance Imaging. 27 (4): 685–91. doi:10.1002/jmri.21049. PMC 2544629. PMID 18302232.
  4. ^ Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau MÉ, et al. (June 2013). "BigBrain: an ultrahigh-resolution 3D human brain model". Science. 340 (6139): 1472–5. Bibcode:2013Sci...340.1472A. doi:10.1126/science.1235381. PMID 23788795.
  5. ^ Kempton MJ, Geddes JR, Ettinger U, Williams SC, Grasby PM (September 2008). "Meta-analysis, database, and meta-regression of 98 structural imaging studies in bipolar disorder". Archives of General Psychiatry. 65 (9): 1017–32. doi:10.1001/archpsyc.65.9.1017. PMID 18762588.
  6. ^ Serag A, Aljabar P, Ball G, Counsell SJ, Boardman JP, Rutherford MA, et al. (February 2012). "Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression". NeuroImage. 59 (3): 2255–65. doi:10.1016/j.neuroimage.2011.09.062. PMID 21985910.
  7. ^ Szalkai B, Kerepesi C, Varga B, Grolmusz V (February 2017). "Parameterizable consensus connectomes from the Human Connectome Project: the Budapest Reference Connectome Server v3.0". Cognitive Neurodynamics. 11 (1): 113–116. arXiv:1602.04776. doi:10.1007/s11571-016-9407-z. PMC 5264751. PMID 28174617.
  8. ^ Laird AR, Lancaster JL, Fox PT (2005). "BrainMap: the social evolution of a human brain mapping database" (PDF). Neuroinformatics. 3 (1): 65–78. doi:10.1385/ni:3:1:065. PMID 15897617.
  9. ^ Mikula S, Trotts I, Stone JM, Jones EG (March 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.
  10. ^ Nielsen, F.A. (2003). The Brede database: a small database for functional neuroimaging NeuroImage 19(2), Presented at the 9th International Conference on Functional Mapping of the Human Brain, June 19--22, 2003, New York, NY.
  11. ^ Papadopoulos Orfanos D, Michel V, Schwartz Y, Pinel P, Moreno A, Le Bihan D, Frouin V (January 2017). "The Brainomics/Localizer database". NeuroImage. 144 (Pt B): 309–314. doi:10.1016/j.neuroimage.2015.09.052. PMID 26455807.
  12. ^ Tyszka JM, Pauli WM (November 2016). "In vivo delineation of subdivisions of the human amygdaloid complex in a high-resolution group template". Human Brain Mapping. 37 (11): 3979–3998. doi:10.1002/hbm.23289. PMC 5087325. PMID 27354150.
  13. ^ Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, et al. (December 2013). "The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository". Journal of Digital Imaging. 26 (6): 1045–57. doi:10.1007/s10278-013-9622-7. PMC 3824915. PMID 23884657.
  14. ^ Sato A, Sekine Y, Saruta C, Nishibe H, Morita N, Sato Y, Sadakata T, Shinoda Y, Kojima T, Furuichi T (October 2008). "Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum". Neural Networks. 21 (8): 1056–69. doi:10.1016/j.neunet.2008.05.004. PMID 18603407.
  15. ^ Van Horn JD, Grethe JS, Kostelec P, Woodward JB, Aslam JA, Rus D, Rockmore D, Gazzaniga MS (2001) The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studiesPhilos Trans R Soc Lond B Biol Sci Aug 29;356(1412):1323-39
  16. ^ "Hippocampome". hippocampome.org. Retrieved 10 August 2016.
  17. ^ Wheeler DW, White CM, Rees CL, Komendantov AO, Hamilton DJ, Ascoli GA (September 2015). "Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus". eLife. 4: e09960. doi:10.7554/eLife.09960. PMC 4629441. PMID 26402459.
  18. ^ Amunts K, Zilles K (December 2015). "Architectonic Mapping of the Human Brain beyond Brodmann". Neuron. 88 (6): 1086–1107. doi:10.1016/j.neuron.2015.12.001. PMID 26687219.
  19. ^ Zilles K, Amunts K (February 2010). "Centenary of Brodmann's map--conception and fate". Nature Reviews. Neuroscience. 11 (2): 139–45. doi:10.1038/nrn2776. PMID 20046193.
  20. ^ "The Kymata Atlas Homepage". The Kymata Atlas. University of Cambridge. Retrieved 11 December 2015.
  21. ^ Kempton MJ, Salvador Z, Munafò MR, Geddes JR, Simmons A, Frangou S, et al. (July 2011). "Structural neuroimaging studies in major depressive disorder. Meta-analysis and comparison with bipolar disorder". Archives of General Psychiatry. 68 (7): 675–90. doi:10.1001/archgenpsychiatry.2011.60. PMID 21727252. see also MRI database at www.depressiondatabase.org
  22. ^ Rosen GD, Williams AG, Capra JA, Connolly MT, Cruz B, Lu L, Airey DC, Kulkarni K, Williams RW (2000) The Mouse Brain Library @ www.mbl.org. Int Mouse Genome Conference 14: 166. www.mbl.org.
  23. ^ Tripathy, Shreejoy; Gerkin, Richard. "NeuroElectro". www.neuroelectro.org. Retrieved 10 August 2016.
  24. ^ Ascoli GA, Donohue DE, Halavi M (August 2007). "NeuroMorpho.Org: a central resource for neuronal morphologies". The Journal of Neuroscience. 27 (35): 9247–51. doi:10.1523/JNEUROSCI.2055-07.2007. PMID 17728438.
  25. ^ Mirsky JS, Nadkarni PM, Healy MD, Miller PL, Shepherd GM (July 1998). "Database tools for integrating and searching membrane property data correlated with neuronal morphology". Journal of Neuroscience Methods. 82 (1): 105–21. doi:10.1016/S0165-0270(98)00049-1. PMID 10223520.
  26. ^ Marcus DS, Wang TH, Parker J, Csernansky JG, Morris JC, Buckner RL (September 2007). "Open Access Series of Imaging Studies (OASIS): cross-sectional MRI data in young, middle aged, nondemented, and demented older adults". Journal of Cognitive Neuroscience. 19 (9): 1498–507. doi:10.1162/jocn.2007.19.9.1498. PMID 17714011.
  27. ^ Poldrack RA, Barch DM, Mitchell JP, Wager TD, Wagner AD, Devlin JT, Cumba C, Koyejo O, Milham MP (Jul 2013). "Toward open sharing of task-based fMRI data: the OpenfMRI project". Frontiers in Neuroinformatics. 7 (12): 12. doi:10.3389/fninf.2013.00012. PMC 3703526. PMID 23847528.
  28. ^ Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, et al. (January 2016). "OMEGA: The Open MEG Archive". NeuroImage. 124 (Pt B): 1182–7. doi:10.1016/j.neuroimage.2015.04.028. PMID 25896932.
  29. ^ Labus JS, Naliboff B, Kilpatrick L, Liu C, Ashe-McNalley C, dos Santos IR, et al. (January 2016). "Pain and Interoception Imaging Network (PAIN): A multimodal, multisite, brain-imaging repository for chronic somatic and visceral pain disorders". NeuroImage. 124 (Pt B): 1232–7. doi:10.1016/j.neuroimage.2015.04.018. PMC 4627849. PMID 25902408.
  30. ^ Conrad MS, Sutton BP, Dilger RN, Johnson RW (September 2014). "An In Vivo Three-Dimensional Magnetic Resonance Imaging-Based Averaged Brain Collection of the Neonatal Piglet (Sus scrofa)". PLOS One. 9 (9): e107650. doi:10.1371/journal.pone.0107650. PMC 4177841. PMID 25254955.
  31. ^ Wang L, Alpert KI, Calhoun VD, Cobia DJ, Keator DB, King MD, et al. (January 2016). "SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration". NeuroImage. 124 (Pt B): 1155–67. doi:10.1016/j.neuroimage.2015.06.065. PMC 4651768. PMID 26142271.
  32. ^ Obeid I, Picone J (2016-05-13). "The Temple University Hospital EEG Data Corpus". Frontiers in Neuroscience. 10: 196. doi:10.3389/fnins.2016.00196. PMC 4865520. PMID 27242402.
  33. ^ Lüsebrink F, Sciarra A, Mattern H, Yakupov R, Speck O (March 2017). "1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm". Scientific Data. 4 (170032): 170032. Bibcode:2017NatSD...470032L. doi:10.1038/sdata.2017.32. PMC 5349250. PMID 28291265.
  34. ^ Gorgolewski KJ, Varoquaux G, Rivera G, Schwartz Y, Ghosh SS, Maumet M, Nichols TE, Poldrack RA, Poline J, Yarkoni T, Margulies DS (Oct 2014). "NeuroVault.org: A web-based repository for collecting and sharing unthresholded statistical maps of the human brain". bioRxiv 010348.
  35. ^ Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, et al. (September 2008). "The neuroscience information framework: a data and knowledge environment for neuroscience". Neuroinformatics. 6 (3): 149–60. doi:10.1007/s12021-008-9024-z. PMC 2661130. PMID 18946742.
  36. ^ "Right Relevance : Neuroscience". www.rightrelevance.com. Right Relevance. Retrieved 10 August 2016.