Mapping brain circuitry with a light microscope.
TLDR
An overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function is presented.Abstract:
The beginning of the 21st century has seen a renaissance in light microscopy and anatomical tract tracing that together are rapidly advancing our understanding of the form and function of neuronal circuits. The introduction of instruments for automated imaging of whole mouse brains, new cell type–specific and trans-synaptic tracers, and computational methods for handling the whole-brain data sets has opened the door to neuroanatomical studies at an unprecedented scale. We present an overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function.read more
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Visible rodent brain-wide networks at single-neuron resolution
TL;DR: Brain-wide optical tomography techniques are summarized, the progress on visible brain neuronal/vascular networks benefit from these novel techniques, and the future technical development is prospected.
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Optimization of GFP Fluorescence Preservation by a Modified uDISCO Clearing Protocol.
TL;DR: This study determined the optimal pH value for optimized uDISCO and validated the clearing performance of the optimized method according to several parameters, including tissue transparency, size changes, and the maintenance of cell morphology, and demonstrated that a-uDISCO enabled the high-quality brain-wide visualization of neuronal structures.
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Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis
Ludovico Silvestri,Marco Paciscopi,Paolo Soda,Filippo Biamonte,Giulio Iannello,Paolo Frasconi,Francesco S. Pavone +6 more
TL;DR: The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments.
Journal ArticleDOI
Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution
Hao Wang,Zhu Qingyuan,Lufeng Ding,Yan Shen,Chao-Yu Yang,Fang Xu,Chang Shu,Yujie Guo,Zhiwei Xiong,Qinghong Shan,Fan Jia,Peng Su,Qianru Yang,Bing Li,Yu-Xiao Cheng,Xiaobin He,Xi Chen,Feng Wu,Feng Wu,Jiang-Ning Zhou,Jiang-Ning Zhou,Fuqiang Xu,Fuqiang Xu,Hua Han,Hua Han,Pak-Ming Lau,Guo-Qiang Bi,Guo-Qiang Bi +27 more
TL;DR: A new microscopy method of Volumetric Imaging with Synchronized on-the-fly-scan and Readout (VISoR) for high-throughput, high-quality brain mapping, combining synchronized scanning beam illumination and oblique imaging over cleared tissue sections in smooth motion, effectively eliminates motion blur to obtain undistorted images.
Journal ArticleDOI
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets.
Adam L. Tyson,Charly V. Rousseau,Christian J. Niedworok,Sepiedeh Keshavarzi,Chryssanthi Tsitoura,Lee Cossell,Molly Strom,Troy W. Margrie +7 more
TL;DR: In this paper, an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware is presented. And the authors demonstrate the applicability and power of their approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.
References
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Book
The Mouse Brain in Stereotaxic Coordinates
TL;DR: The 3rd edition of this atlas is now in more practical 14"x11" format for convenient lab use and includes a CD of all plates and diagrams, as well as Adobe Illustrator files of the diagrams, and a variety of additional useful material.
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Two-Photon Laser Scanning Fluorescence Microscopy
TL;DR: The fluorescence emission increased quadratically with the excitation intensity so that fluorescence and photo-bleaching were confined to the vicinity of the focal plane as expected for cooperative two-photon excitation.
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Distributed Hierarchical Processing in the Primate Cerebral Cortex
TL;DR: A summary of the layout of cortical areas associated with vision and with other modalities, a computerized database for storing and representing large amounts of information on connectivity patterns, and the application of these data to the analysis of hierarchical organization of the cerebral cortex are reported on.
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A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Linda Madisen,Theresa A. Zwingman,Susan M. Sunkin,Seung Wook Oh,Hatim A. Zariwala,Hong Gu,Lydia Ng,Richard D. Palmiter,Michael Hawrylycz,Allan R. Jones,Ed S. Lein,Hongkui Zeng +11 more
TL;DR: A set of Cre reporter mice with strong, ubiquitous expression of fluorescent proteins of different spectra is generated and enables direct visualization of fine dendritic structures and axonal projections of the labeled neurons, which is useful in mapping neuronal circuitry, imaging and tracking specific cell populations in vivo.
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Genome-wide atlas of gene expression in the adult mouse brain
Ed S. Lein,Michael Hawrylycz,Nancy Ao,Mikael Ayres,Amy Bensinger,Amy Bernard,Andrew F. Boe,Mark S. Boguski,Mark S. Boguski,Kevin S. Brockway,Emi J. Byrnes,Lin Chen,Li Chen,Tsuey-Ming Chen,Mei Chi Chin,Jimmy Chong,Brian E. Crook,Aneta Czaplinska,Chinh Dang,Suvro Datta,Nick Dee,Aimee L. Desaki,Tsega Desta,Ellen Diep,Tim A. Dolbeare,Matthew J. Donelan,Hong-Wei Dong,Jennifer G. Dougherty,Ben J. Duncan,Amanda Ebbert,Gregor Eichele,Lili K. Estin,Casey Faber,Benjamin A.C. Facer,Rick Fields,Shanna R. Fischer,Tim P. Fliss,Cliff Frensley,Sabrina N. Gates,Katie J. Glattfelder,Kevin R. Halverson,Matthew R. Hart,John G. Hohmann,Maureen P. Howell,Darren P. Jeung,Rebecca A. Johnson,Patrick T. Karr,Reena Kawal,Jolene Kidney,Rachel H. Knapik,Chihchau L. Kuan,James H. Lake,Annabel R. Laramee,Kirk D. Larsen,Christopher Lau,Tracy Lemon,Agnes J. Liang,Ying Liu,Lon T. Luong,Jesse Michaels,Judith J. Morgan,Rebecca J. Morgan,Marty Mortrud,Nerick Mosqueda,Lydia Ng,Randy Ng,Geralyn J. Orta,Caroline C. Overly,Tu H. Pak,Sheana Parry,Sayan Dev Pathak,Owen C. Pearson,Ralph B. Puchalski,Zackery L. Riley,Hannah R. Rockett,Stephen A. Rowland,Joshua J. Royall,Marcos J. Ruiz,Nadia R. Sarno,Katherine Schaffnit,Nadiya V. Shapovalova,Taz Sivisay,Clifford R. Slaughterbeck,Simon Smith,Kimberly A. Smith,Bryan I. Smith,Andy J. Sodt,Nick N. Stewart,Kenda-Ruth Stumpf,Susan M. Sunkin,Madhavi Sutram,Angelene Tam,Carey D. Teemer,Christina Thaller,Carol L. Thompson,Lee R. Varnam,Axel Visel,Axel Visel,Ray M. Whitlock,Paul Wohnoutka,Crissa K. Wolkey,Victoria Y. Wong,Matthew J.A. Wood,Murat B. Yaylaoglu,Rob Young,Brian L. Youngstrom,Xu Feng Yuan,Bin Zhang,Theresa A. Zwingman,Allan R. Jones +109 more
TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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