Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy

In this photo essay, we present a sampling of technologies from laboratories at the forefront of whole-brain clearing and imaging for high-resolution analysis of cell populations and neuronal circuits. The data presented here were provided for the eponymous Mini-Symposium presented at the Society for Neuroscience's 2018 annual meeting.

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[5]  Kwanghun Chung,et al.  Simultaneous protection of tissue physicochemical properties using polyfunctional crosslinkers , 2018, Nature Biotechnology.

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[7]  Viviana Gradinaru,et al.  Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow , 2017, Science Translational Medicine.

[8]  Hiroki R Ueda,et al.  Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling. , 2016, Annual review of cell and developmental biology.

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

[10]  Frank Bradke,et al.  Three-dimensional imaging of solvent-cleared organs using 3 DISCO , 2012 .

[11]  Rajan P Kulkarni,et al.  Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing , 2014, Cell.

[12]  Sripriya Ravindra Kumar,et al.  Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration , 2018, bioRxiv.

[13]  Hans-Ulrich Dodt,et al.  3D‐ultramicroscopy utilizing aspheric optics , 2014, Journal of biophotonics.

[14]  V. Gradinaru,et al.  Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems , 2017, Nature Neuroscience.

[15]  Dimitri Perrin,et al.  Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization , 2014, Cell.

[16]  Michael Z. Lin,et al.  Cell-Type-Specific Optical Recording of Membrane Voltage Dynamics in Freely Moving Mice , 2016, Cell.

[17]  Charless C. Fowlkes,et al.  Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping , 2015, Nature Protocols.

[18]  V. Gradinaru,et al.  Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology? , 2017, BMC Biology.

[19]  Viviana Gradinaru,et al.  Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. , 2016, Current opinion in biotechnology.

[20]  Niles A. Pierce,et al.  Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability , 2014, ACS nano.

[21]  Atsushi Miyawaki,et al.  Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain , 2011, Nature Neuroscience.

[22]  Viviana Gradinaru,et al.  Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing , 2016, Development.

[23]  Sripriya Ravindra Kumar,et al.  Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain , 2015, Nature Biotechnology.

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

[25]  Kohei Miyazono,et al.  Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution. , 2017, Cell reports.

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

[27]  Karl Deisseroth,et al.  Hydrogel-Tissue Chemistry: Principles and Applications. , 2018, Annual review of biophysics.

[28]  Atsushi Miyawaki,et al.  ScaleS: an optical clearing palette for biological imaging , 2015, Nature Neuroscience.

[29]  Kwanghun Chung,et al.  Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues , 2016, Nature Biotechnology.

[30]  Kwanghun Chung,et al.  Stochastic electrotransport selectively enhances the transport of highly electromobile molecules , 2015, Proceedings of the National Academy of Sciences.

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

[32]  Haruo Kasai,et al.  Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents. , 2018, Cell reports.

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

[34]  Bjoern H Menze,et al.  Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice , 2018, bioRxiv.

[35]  Kwanghun Chung,et al.  Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems , 2015, Cell.

[36]  Hiroshi Sekiya,et al.  A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing , 2018, Nature Neuroscience.

[37]  Yaniv Ziv,et al.  Time-lapse imaging of disease progression in deep brain areas using fluorescence microendoscopy , 2011, Nature Medicine.