title: Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.
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.
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Renier
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Eliza L
authors.initials: EL
authors.lastname: Adams
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Christoph
authors.initials: C
authors.lastname: Kirst
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Zhuhao
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Azevedo
authors.affiliation: Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Johannes
authors.initials: J
authors.lastname: Kohl
authors.affiliation: Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Anita E
authors.initials: AE
authors.lastname: Autry
authors.affiliation: Certerra, Cold Spring Harbor, NY 11724, USA.
authors.forename: Lolahon
authors.initials: L
authors.lastname: Kadiri
authors.affiliation: Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA; Certerra, Cold Spring Harbor, NY 11724, USA.
authors.forename: Kannan
authors.initials: K
authors.lastname: Umadevi Venkataraju
authors.affiliation: Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA.
authors.forename: Victoria X
authors.initials: VX
authors.lastname: Wang
authors.affiliation: Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA.
authors.forename: Cheuk Y
authors.initials: CY
authors.lastname: Tang
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Olav
authors.initials: O
authors.lastname: Olsen
authors.affiliation: Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Dulac
authors.affiliation: Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Osten
authors.affiliation: Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. Electronic address: marctl@rockefeller.edu.
authors.forename: Marc
authors.initials: M
authors.lastname: Tessier-Lavigne
mesh_terms: D000818:Animals; D014150:Antipsychotic Agents / Q000008:administration & dosage; D001522:Behavior, Animal; D001921:Brain / Q000378:metabolism; D005106:Exploratory Behavior; D017781:Genes, Immediate-Early; D006220:Haloperidol / Q000008:administration & dosage; D007150:Immunohistochemistry; D051379:Mice; D008810:Mice, Inbred C57BL; D059906:Neuroimaging / Q000379:methods*
chemical_list: D014150:Antipsychotic Agents; D006220:Haloperidol