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Cell. 2016 Jun 16;165(7):1789-1802. doi: 10.1016/j.cell.2016.05.007. Epub 2016 May 26.

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.

Author information

1
Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
2
Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
3
Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
4
Certerra, Cold Spring Harbor, NY 11724, USA.
5
Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA; Certerra, Cold Spring Harbor, NY 11724, USA.
6
Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA.
7
Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA.
8
Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. Electronic address: marctl@rockefeller.edu.

Abstract

Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization, and quantification of the activity of all neurons across the entire brain, which has not, to date, been achieved in the mammalian brain. We introduce a pipeline for high-speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Last, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available.

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PMID:
27238021
PMCID:
PMC4912438
DOI:
10.1016/j.cell.2016.05.007
[Indexed for MEDLINE]
Free PMC Article

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