Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains

Year: 2015

Authors: Muellenbroich M.C., Silvestri L., Onofri L., Costantini I., Van’t Hoff M., Sacconi L., Iannello G., Pavone F.S.

Autors Affiliation: University of Florence, European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino (FI) Italy;
University of Florence, departament of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino (FI) 50019 Italy; National Institute of Optics (INO-CNR), Via Nello Carrara 1, Sesto Fiorentino (FI) 50019 Italy; University Campus Bio-medico of Rome v. Alvaro del Portillo 21, Roma 00128, Italy; Internetaional Centre of Computational Neurophotonics Via Nello Carrara 1, Sesto Fiorentino (FI)Italy

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. (C) The Authors.


Volume: 2 (4)      Pages from: 041404-1  to: 041404-13

More Information: The authors are grateful to Riccardo Ballerini and Ahmed Hajeb from the mechanics workshop at LENS for fabrication of the sample chamber. We further thank Marco De Pas from the electronic workshop for his expertize in the fabrication of the custom-made amplification electronics. We thank GARR for the 10-GB optical fibre connection to CINECA and CINECA for hosting our data. The research leading to these results has received funding from the European Union Seventh Framework Program (FP7/2007-2013) under grant agreements No. 604102 (Human Brain Project) and No. 284464 (LASERLAB-EUROPE). The research has also been supported by the Italian Ministry for Education, University, and Research in the framework of the Flagship Project NanoMAX, by “Ente Cassa di Risparmio di Firenze” (private foundation). Research activities were also supported by Regione Toscana in the program POR-CreO 2007-2013 (Linea di interventi 1.5.a-1.6-Bando Unico R&S 2012) under grant agreement (CUP) No. 6408.30122011.026000201. M.v. H has a financial interest in Murmex by Distrio, Amsterdam, the Netherlands.
KeyWords: Brain mapping; Computer programming languages; Data handling; Digital storage; Information management; Mammals; Microscopes; Throughput, High-Throughput Imaging; Light-sheet microscopies; Selective plane illuminations; Software management; Whole brains, Big data, adult; animal experiment; Animal tissue; Article; Brain tissue; Computer analysis; Controlled study; Data analysis software; Fluorescence analysis; High throughput light sheet microscopy; Illumination; Information processing; Managed care; Mathematical analysis; Microscopy; Mouse; Neuroanatomy; Neuroimaging; Nonhuman; Optics; Pipeline; Structure analysis; Three dimensional imaging; Transgenic mouse
DOI: 10.1117/1.NPh.2.4.041404

Citations: 17
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