Three-dimensional, isotropic imaging of mouse brain using multi-view deconvolution light sheet microscopy

We present a three-dimensional (3D) isotropic imaging of mouse brain using light-sheet fluorescent microscopy (LSFM) in conjunction with a multi-view imaging computation. Unlike common single view LSFM is used for mouse brain imaging, the brain tissue is 3D imaged under eight views in our study, by a home-built selective plane illumination microscopy (SPIM). An output image containing complete structural information as well as significantly improved resolution (∼4 times) are then computed based on these eight views of data, using a bead-guided multi-view registration and deconvolution. With superior imaging quality, the astrocyte and pyramidal neurons together with their subcellular nerve fibers can be clearly visualized and segmented. With further including other computational methods, this study can be potentially scaled up to map the connectome of whole mouse brain with a simple light-sheet microscope.

[1]  Citlali Pérez Campos,et al.  High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics , 2013, Nature Communications.

[2]  N. Plesnila,et al.  Shrinkage-mediated imaging of entire organs and organisms using uDISCO , 2016, Nature Methods.

[3]  Ernst H. K. Stelzer,et al.  High-resolution deep imaging of live cellular spheroids with light-sheet-based fluorescence microscopy , 2013, Cell and Tissue Research.

[4]  Jeremy Freeman,et al.  Light-sheet imaging for systems neuroscience , 2014, Nature Methods.

[5]  W. Denk,et al.  Deep tissue two-photon microscopy , 2005, Nature Methods.

[6]  Jan Huisken,et al.  Zebrafish model for human long QT syndrome , 2007, Proceedings of the National Academy of Sciences.

[7]  K. Deisseroth,et al.  Advanced CLARITY for rapid and high-resolution imaging of intact tissues , 2014, Nature Protocols.

[8]  T. Holy,et al.  Fast Three-Dimensional Fluorescence Imaging of Activity in Neural Populations by Objective-Coupled Planar Illumination Microscopy , 2008, Neuron.

[9]  C.-C. Jay Kuo,et al.  Amendment history : Corrigendum ( August 2016 ) 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation , 2018 .

[10]  D. Stainier,et al.  Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). , 2007, Optics letters.

[11]  Stephan Saalfeld,et al.  Software for bead-based registration of selective plane illumination microscopy data , 2010, Nature Methods.

[12]  F. Del Bene,et al.  Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy , 2004, Science.

[13]  A. Schierloh,et al.  Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain , 2007, Nature Methods.

[14]  Shaoqun Zeng,et al.  High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level , 2016, Nature Communications.

[15]  Stephan Preibisch,et al.  Efficient Bayesian-based multiview deconvolution , 2013, Nature Methods.

[16]  Jan Huisken,et al.  Multi-view image fusion improves resolution in three-dimensional microscopy. , 2007, Optics express.

[17]  Hao Jiang,et al.  Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope. , 2016, Biomedical optics express.

[18]  Hang Zhou,et al.  NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites , 2015, Nature Methods.

[19]  Dimitri Perrin,et al.  Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging , 2015, Nature Protocols.

[20]  M. Davidson,et al.  Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination , 2011, Nature Methods.

[21]  Philipp J. Keller,et al.  Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[22]  Wesley R. Legant,et al.  Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution , 2014, Science.

[23]  Jan Huisken,et al.  Selective plane illumination microscopy techniques in developmental biology , 2009, Development.

[24]  H. Dodt,et al.  Ultramicroscopy: 3D reconstruction of large microscopical specimens , 2008, Journal of biophotonics.

[25]  Matthias Hillenbrand,et al.  Thin-sheet laser imaging microscopy for optical sectioning of thick tissues. , 2009, BioTechniques.

[26]  Hans-Ulrich Dodt,et al.  Reduction of Photo Bleaching and Long Term Archiving of Chemically Cleared GFP-Expressing Mouse Brains , 2014, PloS one.

[27]  Philipp J. Keller,et al.  Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy , 2010, Nature Methods.

[28]  Benjamin Schmid,et al.  High-resolution reconstruction of the beating zebrafish heart , 2014, Nature Methods.

[29]  Misha B. Ahrens,et al.  Visualizing Whole-Brain Activity and Development at the Single-Cell Level Using Light-Sheet Microscopy , 2015, Neuron.

[30]  F. Wise,et al.  In vivo three-photon microscopy of subcortical structures within an intact mouse brain , 2012, Nature Photonics.

[31]  Philipp J. Keller,et al.  Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy , 2012, Nature Methods.

[32]  E. Susaki,et al.  Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis , 2014, Cell.

[33]  Philipp J. Keller,et al.  Whole-brain functional imaging at cellular resolution using light-sheet microscopy , 2013, Nature Methods.