Biology:List of neuroscience databases

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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]

Neuroscience databases

Name Description Organism Level (gene, neuron, macroscopic) Data (MRI, fMRI, images, descriptive, numerical) Disorder Register 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 Lesions Research 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. Rat Macroscopic Video Obsessive-compulsive disorder No [2]
Allen Brain Atlas Atlas, stained sections from brains showing development and gene expression Mouse, Human Macroscopic, Gene Images Healthy No [3]
Alzheimer's Disease Neuroimaging Initiative (ADNI) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's disease Yes [4]
Big Brain 3D reconstruction of complete brain from cell-body stained histology sections at 20 micron isotropic resolution Human Microscopic Images Healthy No [5]
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 [6]
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-CODE A multi-modal, cross-disorder platform for integrated neuroscience research and data by the Ontario Brain Institute. Human, Animal Multimodal datasets (clinical, imaging, molecular, etc.) Descriptive, numerical, imaging, molecular, genetics Neurodevelopmental, Cerebral Palsy, Epilepsy, Depression, Neurodegeneration, Concussion Yes [7]
Brain-Development.org Structural MRI images and Atlases Human Macroscopic MRI datasets Fetuses, healthy and prematurely born neonates Yes [8]
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 [9]
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 [10]
BrainMaps Atlas, high resolution stained sections from brains Human, primate and non-primate (14 species in all) Neuron and Macroscopic Images Healthy No [11]
Brain/MINDS Dataportal Atlas, in-vivo and ex-vivo MRI scans, ECoG recordings Common Marmoset, Human Macroscopic Images Healthy No [12]
Brede Database fMRI and PET coordinate database Human Macroscopic Descriptive Healthy No [13]
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 [14]
BuzLabDB: The Buzsaki Lab Databank Electrophysiological recordings performed in freely moving rats and mice collected by investigators in the Buzsaki Lab Mice and rats Multiscale Spike trains, LFP, Raw ephys data Healthy No [15][16]
Caltech Subcortical Atlas MRI scans Human Macroscopic MRI Healthy No [17]
Cambridge Centre for Ageing and Neuroscience (Cam-CAN) MRI, fMRI, MEG data for ~700 population-derived healthy adults aged 18–88 Human Macroscopic Images, Descriptive, Numerical Healthy No [18]
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 [19]
Cerebellar Development Transcriptome Database Atlas, stained sections from mouse brains showing cerebellar development and gene expression Mouse Macroscopic, Gene Images Healthy No [20]
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
DANDI: Distributed Archives for Neurophysiology Data Integration cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments Human and several other species Multiscale Spike trains, LFP, MUA, MRI Healthy
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 [21]
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 [22][23]
IBA: Infant Brain Atlas Infant brain atlases from 2 weeks to 2 years of age Human infants Macroscopic, microscopic, brain regions MRI Healthy No [24]
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
In vivo human phantom Ultrahigh 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 decade Human Mesoscopic Structural MRI with various contrasts, microstructure MRI and functional MRI Healthy No [25]
JuBrain atlas Probabilistic cytoarchitectonic 3D maps of the human brain Human Mesoscopic Structural Healthy No [26][27]
Kymata Atlas Functional atlas of the human cortex Human Macroscopic Functional Healthy No [28]
Major Depressive Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Major Depressive Disorder No [29]
Marmoset Gene Atlas Gene expression in the common marmoset whole brain Common Marmoset Macroscopic, Gene Images Healthy No [30]
Mouse Brain Library Atlas, stained sections from mouse brains Mouse Macroscopic Images Healthy No [31]
MouseLight Complete, whole-brain reconstructions Mouse Neuron Cell morphology, projectome connectivity Healthy No [32]
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 [33]
Neuromorpho.org 3D models of real neurons Human, rat, mouse, monkey, others Neuron Images and 3D data Healthy No [34]
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 [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, 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 [36]
Open Connectome Project Database of different circuitry frameworks and neuroimaging datasets, including volumetric datasets, atlases, and connectomics research Human, mouse, bat, zebrafish, insect, other Multilevel: brain regions, connections, neurons, gene expression patterns Images and 3D data Healthy No [37]
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 [38]
Open MEG Archive (OMEGA) Magnetoencephalography, structural MRI datasets, and demographics Human Macroscopic MEG, T1 MRI datasets, demographic data Healthy, ADHD, Traumatic brain injury Yes [39]
The PAIN Repository Structural, Diffusion and Functional MRI datasets Human Human Macroscopic MRI datasets and Metadata Healthy and Pain Conditions Yes [40]
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 [41]
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 [42]
Temple EEG Database Over 30,000 clinical EEGs and accompanying neurologist reports Human Macroscopic EEG Healthy and various diseases Yes [43]
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 [44]
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 [45]

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 [46]

Neuroscience article aggregators

Neuroscience feed at RightRelevance.[47]

See also

References

  1. ↑ "Number of entries using search query 'database'". NIF. https://neuinfo.org/mynif/search.php?q=database&first=true&t=indexable&nif=nlx_144509-1. 
  2. ↑ Szechtman H, Dvorkin-Gheva A, Gomez-Marin A (September 21, 2022). Supporting data for "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 Lesions". GigaScience Database. doi:10.5524/102261. http://dx.doi.org/10.5524/102261. 
  3. ↑ "Genome-wide atlas of gene expression in the adult mouse brain". Nature 445 (7124): 168–76. January 2007. doi:10.1038/nature05453. PMID 17151600. Bibcode: 2007Natur.445..168L. 
  4. ↑ "The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods". Journal of Magnetic Resonance Imaging 27 (4): 685–91. April 2008. doi:10.1002/jmri.21049. PMID 18302232. 
  5. ↑ "BigBrain: an ultrahigh-resolution 3D human brain model". Science 340 (6139): 1472–5. June 2013. doi:10.1126/science.1235381. PMID 23788795. Bibcode: 2013Sci...340.1472A. 
  6. ↑ "Meta-analysis, database, and meta-regression of 98 structural imaging studies in bipolar disorder". Archives of General Psychiatry 65 (9): 1017–32. September 2008. doi:10.1001/archpsyc.65.9.1017. PMID 18762588. 
  7. ↑ "Brain-CODE: A Secure Neuroinformatics Platform for Management, Federation, Sharing and Analysis of Multi-Dimensional Neuroscience Data". Frontiers in Neuroinformatics 12: 28. 2018. doi:10.3389/fninf.2018.00028. ISSN 1662-5196. PMID 29875648. 
  8. ↑ "Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression". NeuroImage 59 (3): 2255–65. February 2012. doi:10.1016/j.neuroimage.2011.09.062. PMID 21985910. 
  9. ↑ "Parameterizable consensus connectomes from the Human Connectome Project: the Budapest Reference Connectome Server v3.0". Cognitive Neurodynamics 11 (1): 113–116. February 2017. doi:10.1007/s11571-016-9407-z. PMID 28174617. 
  10. ↑ "BrainMap: the social evolution of a human brain mapping database". Neuroinformatics 3 (1): 65–78. 2005. doi:10.1385/ni:3:1:065. PMID 15897617. http://brainmap.org/pubs/LairdNI05.pdf. 
  11. ↑ "Internet-enabled high-resolution brain mapping and virtual microscopy". NeuroImage 35 (1): 9–15. March 2007. doi:10.1016/j.neuroimage.2006.11.053. PMID 17229579. 
  12. ↑ "Brain/MINDS: A Japanese National Brain Project for Marmoset Neuroscience". Neuron 92 (3): 582–590. November 2016. doi:10.1016/j.neuron.2016.10.018. PMID 27809998. 
  13. ↑ 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.
  14. ↑ "The Brainomics/Localizer database". NeuroImage 144 (Pt B): 309–314. January 2017. doi:10.1016/j.neuroimage.2015.09.052. PMID 26455807. https://hal-cea.archives-ouvertes.fr/cea-01213448. 
  15. ↑ Petersen, Peter Christian; Hernandez, Michelle; Buzsáki, György (2020). The Buzsaki Lab Databank – Public electrophysiological datasets from awake animals. doi:10.5281/zenodo.4307883. https://doi.org/10.5281/zenodo.4307883. 
  16. ↑ "The Buzsaki Lab databank". https://buzsakilab.com/wp/database/. 
  17. ↑ "In vivo delineation of subdivisions of the human amygdaloid complex in a high-resolution group template". Human Brain Mapping 37 (11): 3979–3998. November 2016. doi:10.1002/hbm.23289. PMID 27354150. 
  18. ↑ "The Cambridge Centre for Ageing and Neuroscience (Cam-CAN) study protocol: a cross-sectional, lifespan, multidisciplinary examination of healthy cognitive ageing". BMC Neurology 14 (6): 204. October 2014. doi:10.1186/s12883-014-0204-1. PMID 25412575. 
  19. ↑ "The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository". Journal of Digital Imaging 26 (6): 1045–57. December 2013. doi:10.1007/s10278-013-9622-7. PMID 23884657. 
  20. ↑ "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. October 2008. doi:10.1016/j.neunet.2008.05.004. PMID 18603407. 
  21. ↑ 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
  22. ↑ "Hippocampome". http://hippocampome.org/php/index.php. 
  23. ↑ "Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus". eLife 4: e09960. September 2015. doi:10.7554/eLife.09960. PMID 26402459. 
  24. ↑ "Multifaceted atlases of the human brain in its infancy". Nature Methods 20 (1): 55–64. 2023. doi:10.1038/s41592-022-01703-z. PMID 36585454. 
  25. ↑ "Comprehensive ultrahigh resolution whole brain in vivo MRI dataset as a human phantom". Scientific Data 8 (1): 138. May 2021. doi:10.1038/s41597-021-00923-w. PMID 34035308. Bibcode: 2021NatSD...8..138L. 
  26. ↑ "Architectonic Mapping of the Human Brain beyond Brodmann". Neuron 88 (6): 1086–1107. December 2015. doi:10.1016/j.neuron.2015.12.001. PMID 26687219. 
  27. ↑ "Centenary of Brodmann's map--conception and fate". Nature Reviews. Neuroscience 11 (2): 139–45. February 2010. doi:10.1038/nrn2776. PMID 20046193. 
  28. ↑ "The Kymata Atlas Homepage". University of Cambridge. https://kymata.org/. 
  29. ↑ "Structural neuroimaging studies in major depressive disorder. Meta-analysis and comparison with bipolar disorder". Archives of General Psychiatry 68 (7): 675–90. July 2011. doi:10.1001/archgenpsychiatry.2011.60. PMID 21727252.  see also MRI database at www.depressiondatabase.org
  30. ↑ "Digital gene atlas of neonate common marmoset brain". Neurosci Res 128: 1–13. March 2018. doi:10.1016/j.neures.2017.10.009. PMID 29111135. 
  31. ↑ 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.
  32. ↑ Winnubst, Johan; Bas, Erhan; Ferreira, Tiago A.; Wu, Zhuhao; Economo, Michael N.; Edson, Patrick; Arthur, Ben J.; Bruns, Christopher et al. (2019-09-19). "Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain". Cell 179 (1): 268–281.e13. doi:10.1016/j.cell.2019.07.042. ISSN 1097-4172. PMID 31495573. 
  33. ↑ Tripathy, Shreejoy; Gerkin, Richard. "NeuroElectro". http://www.neuroelectro.org/. 
  34. ↑ "NeuroMorpho.Org: a central resource for neuronal morphologies". The Journal of Neuroscience 27 (35): 9247–51. August 2007. doi:10.1523/JNEUROSCI.2055-07.2007. PMID 17728438. 
  35. ↑ "Database tools for integrating and searching membrane property data correlated with neuronal morphology". Journal of Neuroscience Methods 82 (1): 105–21. July 1998. doi:10.1016/S0165-0270(98)00049-1. PMID 10223520. 
  36. ↑ "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. September 2007. doi:10.1162/jocn.2007.19.9.1498. PMID 17714011. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33896768. 
  37. ↑ Vogelstein, Joshua T (2011-11-18). "Q&A: What is the Open Connectome Project?". Neural Systems & Circuits 1 (1): 16. doi:10.1186/2042-1001-1-16. ISSN 2042-1001. PMID 22329952. 
  38. ↑ "Toward open sharing of task-based fMRI data: the OpenfMRI project". Frontiers in Neuroinformatics 7 (12): 12. Jul 2013. doi:10.3389/fninf.2013.00012. PMID 23847528. 
  39. ↑ "OMEGA: The Open MEG Archive". NeuroImage 124 (Pt B): 1182–7. January 2016. doi:10.1016/j.neuroimage.2015.04.028. PMID 25896932. 
  40. ↑ "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. January 2016. doi:10.1016/j.neuroimage.2015.04.018. PMID 25902408. 
  41. ↑ "An In Vivo Three-Dimensional Magnetic Resonance Imaging-Based Averaged Brain Collection of the Neonatal Piglet (Sus scrofa)". PLOS ONE 9 (9): e107650. September 2014. doi:10.1371/journal.pone.0107650. PMID 25254955. Bibcode: 2014PLoSO...9j7650C. 
  42. ↑ "SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration". NeuroImage 124 (Pt B): 1155–67. January 2016. doi:10.1016/j.neuroimage.2015.06.065. PMID 26142271. 
  43. ↑ "The Temple University Hospital EEG Data Corpus". Frontiers in Neuroscience 10: 196. 2016-05-13. doi:10.3389/fnins.2016.00196. PMID 27242402. 
  44. ↑ "1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm". Scientific Data 4 (170032): 170032. March 2017. doi:10.1038/sdata.2017.32. PMID 28291265. Bibcode: 2017NatSD...470032L. 
  45. ↑ 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.
  46. ↑ "The neuroscience information framework: a data and knowledge environment for neuroscience". Neuroinformatics 6 (3): 149–60. September 2008. doi:10.1007/s12021-008-9024-z. PMID 18946742. PMC 2661130. http://neuinfo.org/about/publications.shtm. 
  47. ↑ "Right Relevance : Neuroscience". Right Relevance. http://www.rightrelevance.com/search/articles?query=neuroscience. 



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