title: Whole Mouse Brain Image Reconstruction from Serial Coronal Sections Using FIJI (ImageJ).
abstract: Whole-brain reconstruction of the mouse enables comprehensive analysis of the distribution of neurochemical markers, the distribution of anterogradely labeled axonal projections or retrogradely labeled neurons projecting to a specific brain site, or the distribution of neurons displaying activity-related markers in behavioral paradigms. This unit describes a method to produce whole-brain reconstruction image sets from coronal brain sections with up to four fluorescent markers using the freely available image-processing program FIJI (ImageJ).
authors.affiliation: Laboratory of Systems Neuroscience, NIMH, Bethesda, Maryland.
authors.forename: Ronald
authors.initials: R
authors.lastname: Paletzki
authors.affiliation: Laboratory of Systems Neuroscience, NIMH, Bethesda, Maryland.
authors.forename: Charles R
authors.initials: CR
authors.lastname: Gerfen
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping; D002540:Cerebral Cortex / Q000166:cytology*; D007091:Image Processing, Computer-Assisted; D051379:Mice; D009448:Neurochemistry; D059906:Neuroimaging / Q000379:methods*; D009474:Neurons / Q000378:metabolism*
keywords: brain reconstruction; imaging; neuroanatomy