Data sources

Table 2: Specific data sources. A star ``*'' indicates that the data source has public data easily available, e.g., through the Internet. The second column refer to Shepherd's levels listed in table 1. See also the The SfN Neuroscience Database Gateway at [Gardner and Shepherd, 2004], Neuroguide web-page on databases:
Name   Description Reference
Allen Brain Atlas * AH Mouse brain atlas of gene transcriptions. In situ hybridization stained 3D images,, [Dong, 2006,Lein et al., 2007,Markram, 2007]
(Old) BrainMapTM * AB Neuroimaging location data. Contains Bibliographic information, experimental descriptors and 3D Talairach coordinates. This ``old'' and closed database is continued as ``BrainMap DBJ'' (which now is referred to as ``BrainMap'') [Fox and Lancaster, 1994,Fox et al., 1994,Fox et al., 1995,Lancaster et al., 1994,Lancaster et al., 1997a,Fox and Lancaster, 2002]
(New) BrainMapTM/ BrainMap DBJ\textregistered* AB Neuroimaging location data. Continuation of (original) BrainMap. As of 2005 referred to as ``BrainMap'' [Fox et al., 2002,Fox and Lancaster, 2002,Fox et al., 2005a,Laird et al., 2005b],
Brede Database * AB Neuroimaging location data, brain region taxonomy, brain function taxonomy. [Nielsen, 2003],,
fMRIDC * (A)B fMRI scanning data, summary images [Van Horn et al., 2001a,Van Horn and Gazzaniga, 2002,Grethe et al., 2001,Van Horn et al., 2003,Van Horn, 2003]
NeuroGenerator AB Database for human brain imaging. [Roland et al., 2001,Svensson and Forsberg, 2002,Halldorsson and Fredriksson, 2002,Svensson et al., 2003,Forsberg, 2003,Forsberg, 2004]
BrainWeb * B Simulated MRIs of the human brain [Cocosco et al., 1997,Kwan et al., 1996,Kwan et al., 1999,Collins et al., 1998]
IBSR * B MGH CMA Internet Brain Segmentation Repository (IBSR). Repository with raw and segmented (GM/WM/CSF) MRI volumes
IBVD * B MGH CMA Internet Brain Volume Database (IBVD). ``Neuroanatomic volumetric observations'', e.g., from MRI morphological studies. [Kennedy et al., 2003,Haselgrove and Kennedy, 2003],
CoCoMac * B Neural connectivity database for the Macaque brain [Stephan et al., 2001,Stephan et al., 2000b,Stephan and Kötter, 1999,Kötter and Wanke, 2005]
``Cat connectivity'' * B Cortico-cortical, thalamo-cortical, and cortico-thalamic connectivity of the cat. Distributed as ASCII and Excel files. [Scannell et al., 1995]
MC-ET * B Simulation data sets for emission tomography
NeSys * B Database of pontine projections to SI cortex in rat [Bjaalie, 2002],
OASIS B Open Access Series of Imaging Studies. Structural MR from 416 subjects.
Thalamic Connectivity Atlas * B Probabilistic mapping of thalamo-cortical connections based on probabilistic diffusion tractography [Behrens et al., 2003a,Behrens et al., 2003b],
XANAT B Neural connectivity [Press et al., 2001b,Olshausen and Press, 1994],
SumsDB B ``Surface Management Systems DataBase'' [Van Essen et al., 2001,Van Essen, 2002,Van Essen et al., 2005,Dickson et al., 2001],
CoCoDat C Database ``Collation of Cortical Data'' -- for ``organization of single cell and microcircuitry data'' [Dyhrfjeld-Johnsen et al., 2001]
WormAtlas CD Complete neuronal connectivity for the small worm C. elegans [Chen et al., 2006],
L-NEURON CD Database with dendritic trees. L-Neuron and ArborVitae are programs. [Ascoli et al., 2001],
Duke-Southampton archive of neuronal morphology D Database with rat hippocampal neurons. [Cannon et al., 1998] * D Neurophysiology database with time-series and histogram data. Java program as entrance and with the data structure used termed ``common data model'' (CDM). Previously called ``Cortical Neuron Net Database''. Associated with BrainML [Gardner et al., 2001b,Gardner et al., 2001a],,
Neocortical microcircuit database * DE(H) Neuron type (anatomical, electrophysiological), neuron connections
WebQTL * H   [Wang et al., 2003,Chesler et al., 2004],
SenseLab * DG Organization of neurons, neurotransmitters, receptors, cellular ionic currents, computation neuroscientific models (GENESIS, NEURON). Separate database for olfactory receptors. [Mirsky et al., 1998,Marenco et al., 1999,Skoufos et al., 1990,Skoufos et al., 2000,Crasto et al., 2003,Marenco et al., 2003,Crasto et al., 2007],
GPCRDB * G A database of G protein-coupled receptors. Ligand dissociation constants, 3D models [Horn et al., 1998,Horn et al., 2001],
LGICdb * G ``The Ligand Gated Ion Channel Database''. [Le Novère and Changeux, 1999,Le Novère and Changeux, 2001,Le Novère and Changeux, 2001],
HPMR * G ``Human Plasma Membrane Receptome''. A database of plasma membrane receptors [Ben-Shlomo et al., 2003],
WormBase GH Gene expression in Caenorhabditis elegans and other worms [Harris et al., 2004,Bieri et al., 2007],
PubMed * -- Bibliographic data within biomedical sciences [Wilbur and Yang, 1996]
CiteSeer * -- Also called ResearchIndex. Index of research articles in PostScript on the Internet [Lawrence et al., 1999]
Publisher's website * --   E.g.,,
Bibliographic databases * -- Special subject databases, e.g., MuSICA (previously ``Music & Brain Information Database'' -- MBI) and ``Copenhagen Neuropsychology Database'' E.g.,,

Researchers in functional neuroimaging typically both acquired (from original experiments) and analyze the data. However, a number of Internet services store data (raw or analyzed), enabling other researchers to reanalyze, meta-analyze: Table 2 lists Internet databases with available neuroscientific data.

Biological pathways may be protein-protein interactions, metabolic pathways, signaling pathways or gene regulatory networks. Biological pathways databases are listed at Some of the databases are aMAZE, KEGG and ``Signal Transduction Knowledge Environment'' (STCK, not public) WikiPathways is a wiki-oriented pathway database with graphical display of the pathways [Pico et al., 2008].

APLYSIA (``APLYSIA Proficienty Lets You Scan Indentifying Attributes'') once available from seems to have been superseded

Neuroscientific data can be voluminous, e.g., A fMRI study can have a size of a gigabyte and a few minutes of a single EEG multi-electrode recordings can generate hundreds of megabyte. Table 3 is an overview of the different types and sizes of data from experimental measurements and associated sources that are collected in neuroscientific databases.

Table 3: Size of data. Table parallel to [Luscombe et al., 2001, table 1].
Name Description Reference
Data source Data size Neuroinformatics topic
Neuroimaging scanning data Gigabytes / study Reanalyses
Neuroimaging summary images Megabyte / study Meta-analyses
    Volume searches
Neuroimaging location data Kilobytes / study Meta-analyses
    volumes searches
Neural connectivity Kilobytes / study Neural network analysis
Literature 11 million Bibliographic searches

Brain images

Table 4 shows some to the web-sites with brain images and programs. These are usually not in any reference (stereotaxic) space. The images are often more applicable for educational purposes rather than research purposes.

A dead link is ``David'' (Online Atlas of Human Anatomy for Clinical Imaging Diagnosis developed by J.-C. Oberson. CT and MRI (T1, T2, PD) labeled sections)

Some of the many books with brain images are [Mai et al., 1997,Talairach and Tournoux, 1988,Heimer, 1994,Moos and Møller, 2001,Damasio, 1995].

Table 4: Brain images -- either on the web, as program or digitized. More brain images listed in [Toga, 2002a, table 1] and at
Name Description Reference
BrainInfo `The Template Atlas' 62 drawings from the longtailed macaque (Macaca fascicularis), nissl, myelin, photographs (unstained), MRI of Macaca fascicularis. Integrated with NeuroNames,,; [Martin and Bowden, 1996,Rauschning, 1983]
GENSAT Gene expression atlas of the mouse brain [Heintz, 2004],
Brain stem (MSU) ``Atlas of the Human Brain Stem'' with axial images
Brain stem (Swenson) ``Atlas of the Brain Stem'' with axial images
The Whole Brain Atlas Extensive site with human brain transversal sections images (and movies) of normal as well as pathological brains in multiple modalities (T1, T2, PD, PET, CT). Navigation and often labeled images, [Johnson and Becker, 1999].
SPL/NSL Anatomy Browser 3D views of segmented human brain [Golland et al., 1998,Anderson et al., 1998,Umans et al., 1997,Kikinis et al., 1996,Shenton et al., 1995]
Atlas of the Sheep Brain Cell and fiber stained sections with optional labeling. Labeled external surface images.
Columbia Brain Atlas MRI and In vivo (PET) and in vitro (autoradiography) molecular neuroimages
Flybrain Images and illustration of Drosophila [Armstrong et al., 1995],
Digital Anatomist Human brain image in sections, surface and 3D views with interactive labels from Seattle [Brinkley and Rosse, 1997],
Neur@nat Human brain images with interactive labels
MBL C57BL/6J Atlas Mouse brain pictures in coronal and horizontal sections with/out grid. C57BL/6J is a specific strain. DBA/2J atlas is also available.,
PET Brain Atlas (PBA) PET images of the normal and diseased human brain. Labeled and unlabel illustrations.
Neuroanatomy Neuroanatomy, A Photografic Study of the Central Nervous System
The NPAC Visible Human Viewer Java applet for viewing the Visible Human data set in coronal, transversal and sagittal sections [Chang et al., 1998]
Comparative Mammalian Brain Collections Photographs of external surfaces of 175 mammalian species, some (stained?) section images
The Human Brain. Dissection of the Real Brain Photographs and labeled drawings of the human brain from the Virtual Hospital
Brain stem of Rhesus Label sections in stereotaxic coordinates with links to BrainInfo [Smith et al., 1972]
The HCIL Visible Human Explorer Not a web application but a SUN computer program to display images from the visible human data set [North and Korn, 1996,North et al., 1996]
  (Items below do not seem (or has not seemed) to work on a Linux system)  
LONI Human atlas Cryosection images from two normal female cadavers. Possible the termed ``Human cryotome data'' and ``LADY'' before. [Toga et al., 1994] (?),
LONI Monkey Atlas Sections and images of 3D models [Cannestra et al., 1997] (?),
LONI Rat Atlas Labeled Coronal, sagittal and transversal cryosections with coordinates [Toga et al., 1995] (?)
DTI Atlas Labeled images of analyzed diffusion tensor images


Table 5: Genetics association databases
Name Description Reference
AlzGene Limited to Alzeimer's disease. Numerical results from published studies are entered and results of meta-analysis are displayed in tables and plots [Bertram et al., 2007]
CGEMS Cancer Genetic Markers of Susceptibility
dbGaP Genome-wide association studies
GAD Genetics Association Database from NIH, [Becker et al., 2004]
HuGE Pub Lit Human Genome Epidemiology (HuGE) Published Literature database, [Lin et al., 2006]
OMIM The text-oriented web-site Online Mendelian Inheritance in Man links gene and genetic disorders, [McKusick, 1998]
PADB Published Association Database automatically extracts text from published association study abstracts. For the studies were this is possible the database can sort them according to risk measure. [Rhee and Lee, 2007]
PDGene Limited to Parkinson's disease.
PharmGKB The Pharmacogenetics and Pharmacogenomics Knowledge Base
SzGene Limited to schizophrenia [Allen et al., 2008]
T1DBase Limited to type 1 diabetes

Finn Årup Nielsen 2010-04-23