title: Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.
abstract: The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.
authors.affiliation: Allen Institute for Brain Science, 551 North 34th Street, Seattle, WA 98103, USA. susans@alleninstitute.org
authors.forename: Susan M
authors.initials: SM
authors.lastname: Sunkin
authors.forename: Lydia
authors.initials: L
authors.lastname: Ng
authors.forename: Chris
authors.initials: C
authors.lastname: Lau
authors.forename: Tim
authors.initials: T
authors.lastname: Dolbeare
authors.forename: Terri L
authors.initials: TL
authors.lastname: Gilbert
authors.forename: Carol L
authors.initials: CL
authors.lastname: Thompson
authors.forename: Michael
authors.initials: M
authors.lastname: Hawrylycz
authors.forename: Chinh
authors.initials: C
authors.lastname: Dang
mesh_terms: D000328:Adult; D000716:Anatomy, Artistic; D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000196:embryology / Q000254:growth & development / Q000378:metabolism*; D003196:Computer Graphics; D016208:Databases, Factual; D020869:Gene Expression Profiling; D006801:Humans; D017403:In Situ Hybridization; D020407:Internet; D051379:Mice; D011323:Primates