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THIS page is devoted to molecular neuroanatomy resources.

Most resources here are expression atlases, but also there are databases, data sets and a few portals to several databases. If you have a resource that you think should be included (or removed) either email [email protected] or just add the phrase "molecular neuroanatomy resource" to the keywords field of any existing resource page. If your resources does not exist in this system then click the REGISTER A RESOURCE link on the left hand menu.

Several resources have special significance and have been incorporated into the Brain-Gene-Expression view, that lists all the relevant mouse data from the mouse genome informatics (MGI), the Allen Brain Atlas, and the Gensat database. Other brain atlases will be incorporated into this view in the future, but you can search these three together now by clicking here: http://neuinfo.org/nif/nifgwt.html?query=Grm1%20cortex&category=Nervous%20System%20Level:Multi-Level

Other gene expression data can be found by searching various brain region names in the microarray data: http://neuinfo.org/nif/nifgwt.html?query=tegmentum&category=Data%20Type:Microarray

It may also be helpful to search through the image databases as many of these show gene expression in various brain regions or cell types: http://neuinfo.org/nif/nifgwt.html?query=synuclein&category=Data%20Type:Images



[edit] Neuroanatomy of Gene Expression Resources Table

Has role Is part of DefiningCitation
Resource:3D Brain Mobile app
Training material
Resource:Cold Spring Harbor Laboratory https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8
Resource:Adult Wistar Rat Atlas Atlas Duke University; North Carolina; USA http://www.civm.duhs.duke.edu/neuro2012ratatlas/
Resource:Allen Brain Atlas API Software application
Source code
Resource:Allen Institute for Brain Science http://www.brain-map.org/api/index.html
Resource:Allen Human Brain Atlas Database
Atlas
Data visualization software
Resource:Allen Institute for Brain Science http://human.brain-map.org/
Resource:Allen Reference Atlas Reference atlas Resource:Allen Institute for Brain Science http://mouse.brain-map.org/static/atlas
Resource:Anatomy Atlases Topical portal
Atlas
Book
Image collection
http://www.anatomyatlases.org/
Resource:Atlases of the Brain Atlas
Training resource
University of Utah; Utah; USA http://library.med.utah.edu/kw/brain_atlas/
Resource:Automated recognition of brain region mentions in neuroscience literature. Data set University of British Columbia; British Columbia; Canada http://www.chibi.ubc.ca/WhiteText/
Resource:Avian Brain Circuitry Database Spatially referenced dataset
Data repository
Image repository
Image collection
Szent Istvan University Faculty of Veterinary Science; Budapest; Hungary http://www.behav.org/abcd/abcd.php
Resource:BAMS Cells Database Resource:Brain Architecture Management System http://brancusi.usc.edu/bkms/
Resource:BAMS Connectivity Database Resource:Brain Architecture Management System http://brancusi.usc.edu/
Resource:Best of the Web: Neuroscience Data set Best of the Web http://botw.org/top/Science/Neuroscience/
Resource:BigBrain LORIS Database Reference atlas McGill University; Montreal; Canada https://bigbrain.loris.ca/main.php
Resource:Bovine Gene Atlas Expression atlas Mississippi State University; Mississippi; USA http://bovineatlas.msstate.edu/
Resource:BraInSitu: A homepage for molecular neuroanatomy Expression atlas
Database
Experimental protocol
Image
National Institute for Basic Biology; Okazaki; Japan http://www.nibb.ac.jp/brish/indexE.html
Resource:Brain Architecture Management System Database
Ontology
Data repository
University of Southern California; California; USA http://brancusi.usc.edu/bkms/
Resource:Brain Architecture Project Topical portal Resource:Cold Spring Harbor Laboratory http://brainarchitecture.org/
Resource:Brain Atlas Database of Japanese Monkey for WWW Atlas
Image collection
Data set
Resource:RIO-DB - Research Information Database http://riodb.ibase.aist.go.jp/brain/index.php?LANG=ENG
Resource:Brain Bee K-12 program resource MIND: Mankind for International Neuroscience Development Inc. http://www.internationalbrainbee.com
Resource:Brain Explorer Atlas and Teaching Tool Atlas
Training resource
Lundbeck Institute http://brainexplorer.org/
Resource:BrainColor: Collaborative Open Labeling Online Resource Knowledge environment resource
Standard specification
Columbia University; New York; USA http://www.braincolor.org/
Resource:BrainInfo Atlas
Database
Topical portal
Standard specification
University of Washington; Washington; USA
University of California at San Diego; California; USA
http://braininfo.rprc.washington.edu
Resource:BrainMaps.org Atlas
Image repository
University of California at Davis; California; USA http://brainmaps.org
Resource:BrainSpan: Atlas of the Developing Human Brain Reference atlas
Expression atlas
Resource:Allen Institute for Brain Science http://brainspan.org/
Resource:Brainscape Data analysis service
Image repository
Database
University of California at San Diego; California; USA http://www.brainscape.org/
Resource:Brodmanns Interactive Atlas Atlas
MRI 2D image
FMRI consulting
Miami Childrens Hospital; Florida; USA
http://www.fmriconsulting.com/brodmann/
Resource:CNS NeuroWIki Wiki Resource:Congress of Neurological Surgeons http://wiki.cns.org
Resource:CoCoMac Database Resource:German Neuroinformatics Node http://cocomac.g-node.org/drupal/
Resource:Common Upper Mammalian Brain Ontology Ontology Resource:International Neuroinformatics Coordinating Facility
Resource:NeuroLex
http://www.incf.org/activities/our-programs/pons/cumbo
Resource:Computational Neuroanatomy Group Topical portal
Software resource
Resource:George Mason University: Krasnow Institute for Advanced Study http://krasnow1.gmu.edu/cn3/index3.html
Resource:Digital Anatomist Interactive Atlases Project Atlas
Training material
University of Washington; Washington; USA http://www9.biostr.washington.edu/da.html
Resource:Duke University NeuroAnatomy Web Resources Curriculum material Duke University; North Carolina; USA http://pathology.duke.edu/files/neuroanat/nawr_index.html
Resource:FLJ Human cDNA Database Database
Biomaterial analysis service
Molecular neuroanatomy resource
Japanese Biological Informatics Consortium
Research Association for Biotechnology in Japan
http://flj.hinv.jp/
Resource:FMA Ontology
Database
University of Washington; Washington; USA http://sig.biostr.washington.edu/projects/fm/
Resource:FlyBrain: An Online Atlas and Database of the Drosophila Nervous System Atlas
Training material
Data processing software
National Institute for Basic Biology; Okazaki; Japan
University of Arizona; Arizona; USA
University of Freiburg; Baden-Wurttemberg; Germany
http://www.flybrain.org/
Resource:George Mason University: Krasnow Institute for Advanced Study Organization portal
Postdoctoral program resource
George Mason University; Virginia; USA http://www.gmu.edu/departments/krasnow/
Resource:Harvard - Oxford Cortical Structural Atlas Reference atlas Harvard University; Massachusetts; USA http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases
Resource:High Resolution Mouse Brain Atlas Atlas Harvard University; Massachusetts; USA http://www.hms.harvard.edu/research/brain/atlas.html
Resource:Human Brain Atlas Atlas
Video resource
Michigan State University; Michigan; USA https://www.msu.edu/~brains/brains/human/index.html
Resource:Human Brain Connectivity Database Bibliography
Data set
Resource:Brain Architecture Project http://mitraweb1.cshl.edu:8080/BrainArchitecture/pages/publications.faces
Resource:Human Nervous System Neuroanatomy Data set
Image collection
Castillo Publishing http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Images%20of%20the%20Human%20Nervous%20System%20-%20Neuroanatomy.html
Resource:HyperBrain Training material
Image collection
Video resource
University of Utah School of Medicine; Utah; USA http://library.med.utah.edu/kw/hyperbrain/
Resource:Institute of Experimental Medicine of the Hungarian Academy of Sciences: Laboratory of Cerebral Cortext Reserach Laboratory portal Institute of Experimental Medicine of the Hungarian Academy of Sciences http://www.koki.hu/main.php?folderID=903
Resource:International Consortium for Brain Mapping Reference atlas
Data repository
Database
Software resource
Resource:Laboratory of Neuro Imaging http://www.loni.usc.edu/ICBM/
Resource:MGH-USC Human Connectome Project Data set
Image collection
Instrument manufacture
Resource:Laboratory of Neuro Imaging
Harvard Medical School; Massachusetts; USA
Resource:NIH Human Connectome Project
http://www.humanconnectomeproject.org/
Resource:MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System Atlas
Training resource
Data processing software
National Institute for Basic Biology; Okazaki; Japan
University of Arizona; Arizona; USA
University of Freiburg; Baden-Wurttemberg; Germany
http://flybrain.neurobio.arizona.edu/
Resource:McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas Reference atlas Resource:McConnell Brain Imaging Center http://www.bic.mni.mcgill.ca/ServicesAtlases/Cyno
Resource:Mouse Atlas Project Atlas
Database
Resource:Laboratory of Neuro Imaging http://www.emouseatlas.org/emap/home.html
Resource:Mouse Brain Architecture Project 3D spatial image
Reference atlas
Resource:Brain Architecture Project http://brainarchitecture.org/mouse/about
Resource:NIH Blueprint NHP Atlas Reference atlas
Expression atlas
Database
Resource:Allen Institute for Brain Science http://www.blueprintnhpatlas.org/
Resource:NVM Software application
Source code
Image analysis software
Resource:Neuromorphometrics http://neuromorphometrics.org:8080/nvm/index.html
Resource:NeuroLex Wiki Resource:Neuroscience Information Framework
Resource:International Neuroinformatics Coordinating Facility
http://neurolex.org/wiki/Main_Page
Resource:Neuroanatomy Atlas Atlas University of South Carolina; South Carolina; USA http://www.cabiatl.com/mricro/anatomy/home.html
Resource:Neuroanatomy and Neuropathology on the Internet Database
Topical portal
Database
Training resource
Atlas
University of Debrecen; Debrecen; Hungary http://www.neuropat.dote.hu/
Resource:Neuroanatomy at UBC 2D spatial image
3D spatial image
Training material
Atlas
Video resource
University of British Columbia; British Columbia; Canada http://www.neuroanatomy.ca/
Resource:Neuromorphometrics Production service resource http://neuromorphometrics.com
Resource:Neuroscience Information Framework Software development tool
Systems interoperability software
Community building portal
Database
Data repository
University of California at San Diego; California; USA http://neuinfo.org
Resource:Neurostruct Segmentation software Heidelberg University; Heidelberg; Germany
Resource:Max Planck Institute of Neurobiology; Martinsried; Germany
http://www.neurostruct.org
Resource:Program on Ontologies of Neural Structures Topical portal
Standard specification
Resource:International Neuroinformatics Coordinating Facility http://pons.incf.org/
Resource:PubBrain Database
Data analysis service
Resource:Poldracklab Portal http://pubbrain.org/
Resource:Rat Brain Atlas of Paxinos and Watson Reference atlas Castillo Publishing http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Rat_Brain_Atlas.html
Resource:Rat Hippocampus Atlas Reference atlas University of Oslo; Oslo; Norway http://cmbn-approd01.uio.no/zoomgen/hippocampus/home.do
Resource:Rhesus Macaque Atlases for Functional and Structural Imaging Studies Atlas University of Wisconsin-Madison; Wisconsin; USA http://brainmap.wisc.edu/monkey.html
Resource:SRI24 Atlas: Normal Adult Brain Anatomy Reference atlas Resource:Stanford Research Institute International http://www.nitrc.org/projects/sri24/
Resource:SVV Data visualization software Massachusetts General Hospital; Massachusetts; USA http://www.nitrc.org/projects/dave1
Resource:Salamons Neuroanatomy and Neurovasculature Web-Atlas Resource Atlas
Training resource
University of California at Los Angeles; California; USA http://www.radnet.ucla.edu/sections/DINR/index.htm
Resource:ScienceBlogs Neurotopia Blog Resource:ScienceBlogs http://scienceblogs.com/neurotopia/
Resource:Sectional Atlas of Human Brain and Spinal Cord Atlas
Training resource
Temple University School of Medicine; Pennsylvania; USA http://isc.temple.edu/neuroanatomy/lab/atlas/S5/
Resource:Subcellular Anatomy Ontology Ontology Resource:Cell Centered Database http://ccdb.ucsd.edu/SAO
Resource:SumsDB Atlas
Database
Data repository
Data analysis service
Image repository
Washington University School of Medicine in St. Louis; Missouri; USA http://sumsdb.wustl.edu/sums/
Resource:Surface-Based Atlases Database
Atlas
Washington University in St. Louis; Missouri; USA http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases
Resource:Synapse Web Atlas
Image collection
Training material
University of Texas at Austin; Texas; USA http://synapses.clm.utexas.edu
Resource:TOADS-CRUISE Brain Segmentation Tools Segmentation software http://www.nitrc.org/projects/toads-cruise/
Resource:Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Data set Norwegian University of Science and Technology; Trondheim; Norway http://www.temporal-lobe.com/
Resource:UW-Madison Neuroscience Resources Training material
Video resource
Book
Image collection
University of Wisconsin-Madison; Wisconsin; USA http://www.neuroanatomy.wisc.edu/
Resource:University of Washington Integrated Brain Project Ontology
Software resource
http://sig.biostr.washington.edu/projects/brain/
Resource:Virtual NeuroMorphology Electronic Database Data set Resource:Computational Neuroanatomy Group http://krasnow1.gmu.edu/L-Neuron/L-Neuron/database/
Resource:WFU PickAtlas Image processing software Wake Forest School of Medicine; North Carolina; USA http://fmri.wfubmc.edu/software/PickAtlas
Resource:Washington University School of Medicine Neuroscience Tutorial Curriculum material
Image collection
Washington University School of Medicine in St. Louis; Missouri; USA http://www.bioon.com/bioline/neurosci/course/index.htm
Resource:Waxholm Space Standard specification Resource:International Neuroinformatics Coordinating Facility http://incf.org/programs/atlasing/projects/waxholm-space
Resource:Webvision - The Organization of the Retina and Visual System Book
Image collection
Blog
University of Utah School of Medicine; Utah; USA http://webvision.med.utah.edu/
Resource:Whole Brain Atlas Atlas
Image repository
Training material
Harvard Medical School; Massachusetts; USA http://www.med.harvard.edu/AANLIB/
Resource:WormAtlas: A Database of Behavioral and Structural Anatomy of C. elegans Atlas
Training material
Albert Einstein College of Medicine; New York; USA http://wormatlas.org
Resource:Zebrafish Brain Atlas Reference atlas
Data repository
Image repository
University College London; London; United Kingdom http://www.ucl.ac.uk/zebrafish-group/zebrafishbrain/index.php
Resource:aVOR Mobile app
Training material
Liberty Information Technology https://itunes.apple.com/us/app/avor/id497245573?mt=8
Resource:celltypes.org Atlas
Database
Image collection
http://celltypes.org/
Resource:neuropathology blog Blog http://neuropathologyblog.blogspot.com/
Resource:​​​WholeSlide Mobile app
Image collection
Data set
Data visualization software
https://itunes.apple.com/us/app/wholeslide/id448006595?ls=1&mt=8

Contributors

Bandrow, Memartone



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.