title: Exploration and visualization of connectivity in the adult mouse brain.
abstract: The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. All data were aligned to a common template in 3D space to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. A suite of computational tools were developed to search and visualize the projection labeling experiments, available at http://connectivity.brain-map.org. We present three use cases illustrating how these publicly-available tools can be used to perform analyses of long range brain region connectivity. The use cases make extensive use of advanced visualization tools integrated with the atlas including projection density histograms, 3D computed anterograde and retrograde projection paths, and multi-specimen projection composites. These tools offer convenient access to detailed axonal projection information in the adult mouse brain and the ability to perform data analysis and visualization of projection fields and neuroanatomy in an integrated manner.
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: DavidF@alleninstitute.org.
authors: David
authors: D
authors: Feng
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: ChrisL@alleninstitute.org.
authors: Chris
authors: C
authors: Lau
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: LydiaN@alleninstitute.org.
authors: Lydia
authors: L
authors: Ng
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: YangL@alleninstitute.org.
authors: Yang
authors: Y
authors: Li
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: LeonardK@alleninstitute.org.
authors: Leonard
authors: L
authors: Kuan
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: SusanS@alleninstitute.org.
authors: Susan M
authors: SM
authors: Sunkin
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: ChinhDa@alleninstitute.org.
authors: Chinh
authors: C
authors: Dang
authors: Allen Institute for Brain Science, Seattle, WA 98103, United States. Electronic address: MikeH@alleninstitute.org.
authors: Michael
authors: M
authors: Hawrylycz
mesh_terms: D000367:Age Factors; D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000502:physiology; D001931:Brain Mapping / Q000379:methods*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D009415:Nerve Net / Q000033:anatomy & histology* / Q000737:chemistry / Q000502:physiology; D009434:Neural Pathways / Q000033:anatomy & histology / Q000737:chemistry / Q000502:physiology
keywords: Digital atlas; Mouse connectivity atlas; Neuronal projection; Virtual tractography