title: Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.
abstract: The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LeonardK@alleninstitute.org.
authors.forename: Leonard
authors.initials: L
authors.lastname: Kuan
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: YangL@alleninstitute.org.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChrisL@alleninstitute.org.
authors.forename: Chris
authors.initials: C
authors.lastname: Lau
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: DavidF@alleninstitute.org.
authors.forename: David
authors.initials: D
authors.lastname: Feng
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: AmyB@alleninstitute.org.
authors.forename: Amy
authors.initials: A
authors.lastname: Bernard
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: SusanS@alleninstitute.org.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Sunkin
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: HongkuiZ@alleninstitute.org.
authors.forename: Hongkui
authors.initials: H
authors.lastname: Zeng
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChinhDa@alleninstitute.org.
authors.forename: Chinh
authors.initials: C
authors.lastname: Dang
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: MikeH@alleninstitute.org.
authors.forename: Michael
authors.initials: M
authors.lastname: Hawrylycz
authors.affiliation: The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LydiaN@alleninstitute.org.
authors.forename: Lydia
authors.initials: L
authors.lastname: Ng
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000502:physiology; D001931:Brain Mapping / Q000379:methods* / Q000639:trends; D006801:Humans; D048088:Informatics / Q000379:methods* / Q000639:trends; D051379:Mice; D008810:Mice, Inbred C57BL
keywords: Digital atlas; Image registration; Mouse connectivity atlas; Neuronal projection; Signal detection