title: Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains.
abstract: Comprehensive mapping and quantification of neuronal projections in the central nervous system requires high-throughput imaging of large volumes with microscopic resolution. To this end, we have developed a confocal light-sheet microscope that has been optimized for three-dimensional (3-D) imaging of structurally intact clarified whole-mount mouse brains. We describe the optical and electromechanical arrangement of the microscope and give details on the organization of the microscope management software. The software orchestrates all components of the microscope, coordinates critical timing and synchronization, and has been written in a versatile and modular structure using the LabVIEW language. It can easily be adapted and integrated to other microscope systems and has been made freely available to the light-sheet community. The tremendous amount of data routinely generated by light-sheet microscopy further requires novel strategies for data handling and storage. To complete the full imaging pipeline of our high-throughput microscope, we further elaborate on big data management from streaming of raw images up to stitching of 3-D datasets. The mesoscale neuroanatomy imaged at micron-scale resolution in those datasets allows characterization and quantification of neuronal projections in unsectioned mouse brains.
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; University of Florence , Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy.
authors.forename: M Caroline
authors.initials: MC
authors.lastname: Müllenbroich
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; National Institute of Optics , National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy.
authors.forename: Ludovico
authors.initials: L
authors.lastname: Silvestri
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; University Campus Bio-Medico of Rome , v. Alvaro del Portillo 21, Roma 00128, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Onofri
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy.
authors.forename: Irene
authors.initials: I
authors.lastname: Costantini
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; University of Florence , Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy.
authors.forename: Marcel Van't
authors.initials: MV
authors.lastname: Hoff
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; National Institute of Optics , National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Sacconi
authors.affiliation: University Campus Bio-Medico of Rome , v. Alvaro del Portillo 21, Roma 00128, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Iannello
authors.affiliation: University of Florence , European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; University of Florence , Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy ; National Institute of Optics , National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy ; International Centre for Computational Neurophotonics , Via Nello Carrara 1, Sesto Fiorentino 50019, Italy.
authors.forename: Francesco S
authors.initials: FS
authors.lastname: Pavone
keywords: data management; high-throughput imaging; light-sheet microscopy; selective plane illumination microscopy; software management; whole brain imaging