Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

doi:10.1016/j.ymeth.2014.12.013

Review

. 2015 Feb:73:4-17.

doi: 10.1016/j.ymeth.2014.12.013. Epub 2014 Dec 20.

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

Leonard Kuan¹, Yang Li², Chris Lau³, David Feng⁴, Amy Bernard⁵, Susan M Sunkin⁶, Hongkui Zeng⁷, Chinh Dang⁸, Michael Hawrylycz⁹, Lydia Ng¹⁰

Affiliations

¹ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LeonardK@alleninstitute.org.
² The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: YangL@alleninstitute.org.
³ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChrisL@alleninstitute.org.
⁴ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: DavidF@alleninstitute.org.
⁵ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: AmyB@alleninstitute.org.
⁶ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: SusanS@alleninstitute.org.
⁷ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: HongkuiZ@alleninstitute.org.
⁸ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChinhDa@alleninstitute.org.
⁹ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: MikeH@alleninstitute.org.
¹⁰ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LydiaN@alleninstitute.org.

PMID: 25536338
DOI: 10.1016/j.ymeth.2014.12.013

Free article

Review

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

Leonard Kuan et al. Methods. 2015 Feb.

Free article

. 2015 Feb:73:4-17.

doi: 10.1016/j.ymeth.2014.12.013. Epub 2014 Dec 20.

Authors

Leonard Kuan¹, Yang Li², Chris Lau³, David Feng⁴, Amy Bernard⁵, Susan M Sunkin⁶, Hongkui Zeng⁷, Chinh Dang⁸, Michael Hawrylycz⁹, Lydia Ng¹⁰

Affiliations

¹ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LeonardK@alleninstitute.org.
² The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: YangL@alleninstitute.org.
³ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChrisL@alleninstitute.org.
⁴ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: DavidF@alleninstitute.org.
⁵ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: AmyB@alleninstitute.org.
⁶ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: SusanS@alleninstitute.org.
⁷ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: HongkuiZ@alleninstitute.org.
⁸ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: ChinhDa@alleninstitute.org.
⁹ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: MikeH@alleninstitute.org.
¹⁰ The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA. Electronic address: LydiaN@alleninstitute.org.

PMID: 25536338
DOI: 10.1016/j.ymeth.2014.12.013

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.

Keywords: Digital atlas; Image registration; Mouse connectivity atlas; Neuronal projection; Signal detection.

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Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

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Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

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