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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High precision automated detection of labeled nuclei in Gigapixel resolution image data of Mouse Brain
Sukhendu Das,Jaikishan Jayakumar,Samik Banerjee,Janani Ramaswamy,Venu Vangala,Keerthi Ram,Partha P. Mitra,Partha P. Mitra +7 more
TL;DR: An unsupervised, iterative algorithm is described, which provides a high performance for a specific problem of detecting Green Fluorescent Protein labeled nuclei in 2D scans of mouse brains and is focused on the complex problem of decomposing strong overlapped objects of interest.
Journal ArticleDOI
Dendritic Domain-Specific Sampling of Long-Range Axons Shapes Feedforward and Feedback Connectivity of L5 Neurons
TL;DR: In this paper , the synaptic connectivity of brain-wide projections onto pyramidal neurons in the visual cortex of mice was assessed using trans-synaptic viral tracing and subcellular optogenetic circuit mapping.
Journal ArticleDOI
Optical Multilayer Interference Tomography Compatible with Tape-Based Serial SEM for Mesoscale Neuroanatomy
Hao Fan,Hao Fan,Dingsan Luo,Jinlong Zhu,Richard Schalek,Zhenxin Chen,Lingxiao Zhao,Renjie Zhou,Minxuan Sun,Guohua Shi,Yangmin Xie,Jeff W. Lichtman,Ruobing Zhang +12 more
TL;DR: In this paper, the complexity of animals' behaviors and intellect relies on decoding the underlying structure and wiring diagram of their brains, and various imaging techniques have been developed to do this.
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Fast volumetric mapping of human brain slices
Luca Pesce,Luca Pesce,Annunziatina Laurino,Annunziatina Laurino,Vladislav Gavryusev,Vladislav Gavryusev,Giacomo Mazzamuto,Giacomo Mazzamuto,Giuseppe Sancataldo,Giuseppe Sancataldo,Marina Scardigli,Marina Scardigli,Matteo Roffilli,Ludovico Silvestri,Ludovico Silvestri,Ludovico Silvestri,Irene Costantini,Irene Costantini,Francesco S. Pavone,Francesco S. Pavone,Francesco S. Pavone +20 more
TL;DR: Volumetric imaging of large sequentially stained human brain slices is performed, labelled for two different neuronal markers NeuN and GAD67, discriminating the inhibitory population and reconstructing the brain connectivity.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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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