List of neuroscience databases

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]

Neuroscience databases

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]
Brain/MINDS Dataportal	Atlas, in-vivo and ex-vivo MRI scans, ECoG recordings	Common Marmoset, Human	Macroscopic	Images	Healthy	No	[10]
Brede Database	fMRI and PET coordinate database	Human	Macroscopic	Descriptive	Healthy	No	[11]
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	[12]
Caltech Subcortical Atlas	MRI scans	Human	Macroscopic	MRI	Healthy	No	[13]
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	[14]
Cerebellar Development Transcriptome Database	Atlas, stained sections from mouse brains showing cerebellar development and gene expression	Mouse	Macroscopic, Gene	Images	Healthy	No	[15]
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	[16]
GLIMPS Project (GLucose IMaging in Parkinsonian Syndromes)	International FDG-PET scan neurodegenerative disease database	Human	Macroscopic	FDG-PET images	Parkinson's disease (PD), Alzheimer's disease (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	[17][18]
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	[19][20]
Kymata Atlas	Functional atlas of the human cortex	Human	Macroscopic	Functional	Healthy	No	[21]
Major Depressive Disorder Neuroimaging Database	Meta-analysis and database of MRI studies	Human	Macroscopic	Descriptive, numerical	Major Depressive Disorder	No	[22]
Marmoset Gene Atlas	Gene expression in the common marmoset whole brain	Common Marmoset	Macroscopic, Gene	Images	Healthy	No	[23]
Mouse Brain Library	Atlas, stained sections from mouse brains	Mouse	Macroscopic	Images	Healthy	No	[24]
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	[25]
Neuromorpho.org	3D models of real neurons	Human, rat, mouse, monkey, others	Neuron	Images and 3D data	Healthy	No	[26]
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	[27]
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, other	Microscopic, macroscopic	Datasets	Healthy and diseased	No
Open Access Series of Imaging Studies (OASIS)	Structural MRI images	Human	Macroscopic	MRI datasets	Healthy and Alzheimer's Disease	Yes	[28]
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 diseases	No	[29]
Open MEG Archive (OMEGA)	Magnetoencephalography, structural MRI datasets, and demographics	Human	Macroscopic	MEG, T1 MRI datasets, demographic data	Healthy, ADHD, Traumatic brain injury	Yes	[30]
The PAIN Repository	Structural, Diffusion and Functional MRI datasets	Human	Human Macroscopic	MRI datasets and Metadata	Healthy and Pain Conditions	Yes	[31]
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	[32]
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 human	Neuron	Electrophysiology, Morphology and 3-d Reconstructions	Healthy	No
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	[33]
Temple EEG Database	Over 30,000 clinical EEGs and accompanying neurologist reports	Human	Macroscopic	EEG	Healthy and various diseases	Yes	[34]
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	[35]
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	[36]

Databases of neuroscience databases

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	[37]

Neuroscience article aggregators

Neuroscience feed at RightRelevance.[38]

See also

• Neuroinformatics
• Budapest Reference Connectome

References

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. S2CID 4421492.
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. S2CID 14122170.
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. S2CID 9747334.
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. Okano H, Sasaki E, Yamamori T, Iriki A, Shimogori T, Yamaguchi Y, Kasai K, Miyawaki A (November 2016). "Brain/MINDS: A Japanese National Brain Project for Marmoset Neuroscience". Neuron. 92 (3): 582–590. doi:10.1016/j.neuron.2016.10.018. PMID 27809998.
11. 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.
12. 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. S2CID 13004274.
13. 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.
14. 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.
15. 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.
16. 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
17. "Hippocampome". hippocampome.org. Retrieved 10 August 2016.
18. 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.
19. 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.
20. 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. S2CID 5278040.
21. "The Kymata Atlas Homepage". The Kymata Atlas. University of Cambridge. Retrieved 11 December 2015.
22. 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
23. Shimogori T, Abe A, Go Y, Hashikawa T, Kishi N, Kikuchi SS, Kita Y, Niimi K, Nishibe H, Okuno M, Saga K, Sakurai M, Sato M, Serizawa T, Suzuki S, Takahashi E, Tanaka M, Tatsumoto S, Toki M, U M, Wang Y, Windak KJ, Yamagishi H, Yamashita K, Yoda T, Yoshida AC, Yoshida C, Yoshimoto T, Okano H (March 2018). "Digital gene atlas of neonate common marmoset brain". Neurosci Res. 128: 1–13. doi:10.1016/j.neures.2017.10.009. PMID 29111135. S2CID 3735944.
24. 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.
25. Tripathy, Shreejoy; Gerkin, Richard. "NeuroElectro". www.neuroelectro.org. Retrieved 10 August 2016.
26. 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. PMC 6673130. PMID 17728438.
27. 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. S2CID 12871618.
28. 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. S2CID 10840552.
29. 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.
30. 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.
31. 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.
32. 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. Bibcode:2014PLoSO...9j7650C. doi:10.1371/journal.pone.0107650. PMC 4177841. PMID 25254955.
33. 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.
34. 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.
35. 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.
36. 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 10.1101/010348.
37. 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.
38. "Right Relevance : Neuroscience". www.rightrelevance.com. Right Relevance. Retrieved 10 August 2016.