Journal ArticleDOI
Micro-Optical Sectioning Tomography to Obtain a High-Resolution Atlas of the Mouse Brain
Anan Li,Hui Gong,Bin Zhang,Qingdi Wang,Cheng Yan,Jingpeng Wu,Qian Liu,Shaoqun Zeng,Qingming Luo +8 more
TLDR
An automated system that allowed three-dimensional mapping of the morphology and spatial location of neurons and traces of neurites in a whole, intact mouse brain is described and it is found that neighboring Purkinje cells stick to each other.Abstract:
The neuroanatomical architecture is considered to be the basis for understanding brain function and dysfunction. However, existing imaging tools have limitations for brainwide mapping of neural circuits at a mesoscale level. We developed a micro-optical sectioning tomography (MOST) system that can provide micrometer-scale tomography of a centimeter-sized whole mouse brain. Using MOST, we obtained a three-dimensional structural data set of a Golgi-stained whole mouse brain at the neurite level. The morphology and spatial locations of neurons and traces of neurites could be clearly distinguished. We found that neighboring Purkinje cells stick to each other.read more
Citations
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Journal ArticleDOI
Structural and molecular interrogation of intact biological systems
Kwanghun Chung,Jenelle Wallace,Sung-Yon Kim,Sandhiya Kalyanasundaram,Aaron S. Andalman,Thomas J. Davidson,Julie J. Mirzabekov,Kelly A. Zalocusky,Joanna Mattis,Aleksandra K. Denisin,Sally Pak,Hannah L. Bernstein,Charu Ramakrishnan,Logan Grosenick,Viviana Gradinaru,Karl Deisseroth +15 more
TL;DR: It is shown that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.
Journal ArticleDOI
Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis
Etsuo A. Susaki,Kazuki Tainaka,Kazuki Tainaka,Dimitri Perrin,Fumiaki Kishino,Takehiro Tawara,Tomonobu M. Watanabe,Chihiro Yokoyama,Hirotaka Onoe,Megumi Eguchi,Shun Yamaguchi,Shun Yamaguchi,Takaya Abe,Hiroshi Kiyonari,Yoshihiro Shimizu,Atsushi Miyawaki,Hideo Yokota,Hiroki R. Ueda +17 more
TL;DR: CUBIC enables time-course expression profiling of whole adult brains with single-cell resolution and develops a whole-brain cell-nuclear counterstaining protocol and a computational image analysis pipeline that enable the visualization and quantification of neural activities induced by environmental stimulation.
Journal ArticleDOI
BigBrain: An Ultrahigh-Resolution 3D Human Brain Model
Katrin Amunts,Claude Lepage,Louis Borgeat,Hartmut Mohlberg,Timo Dickscheid,M. Rousseau,Sebastian Bludau,Pierre-Louis Bazin,Lindsay B. Lewis,Ana-Maria Oros-Peusquens,Nadim Joni Shah,Thomas Lippert,Karl Zilles,Alan C. Evans +13 more
TL;DR: BigBrain is a free, publicly available tool that provides considerable neuroanatomical insight into the human brain, thereby allowing the extraction of microscopic data for modeling and simulation, and enables testing of hypotheses on optimal path lengths between interconnected cortical regions or on spatial organization of genetic patterning.
Journal ArticleDOI
CLARITY for mapping the nervous system
Kwanghun Chung,Karl Deisseroth +1 more
TL;DR: Hydrogel-based structures can be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue, creating a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins and nucleic acids, and that is permeable to both visible-spectrum photons and exogenous macromolecules.
Journal ArticleDOI
Serial two-photon tomography for automated ex vivo mouse brain imaging
Timothy Ragan,Lolahon R. Kadiri,Kannan Umadevi Venkataraju,Karsten Bahlmann,Jason Sutin,Julian Taranda,Ignacio Arganda-Carreras,Yongsoo Kim,H. Sebastian Seung,Pavel Osten +9 more
TL;DR: An automated method is described that achieves high-throughput fluorescence imaging of mouse brains by integrating two-photon microscopy and tissue sectioning, which opens the door to routine systematic studies of neuroanatomy in mouse models of human brain disorders.
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.
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.
Book
Gray's Anatomy : The Anatomical Basis of Clinical Practice
TL;DR: The Anatomical Nomenclature of the Nervous System and Systemic Overview of the Endocrine System, Principles of Hormone Production and Secretion and Development of the Cardiovascular and Lymphatic Systems are presented.
Journal ArticleDOI
Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP.
Guoping Feng,Rebecca H. Mellor,Michael L. Bernstein,Cynthia Keller-Peck,Quyen T. Nguyen,Mia Wallace,Jeanne M. Nerbonne,Jeff W. Lichtman,Joshua R. Sanes +8 more
TL;DR: Each of 25 independently generated transgenic lines expressed XFP in a unique pattern, even though all incorporated identical regulatory elements (from the thyl gene), for example, all retinal ganglion cells or many cortical neurons were XFP positive in some lines, whereas only a few ganglions or only layer 5 cortical pyramids were labeled in others.
Related Papers (5)
Structural and molecular interrogation of intact biological systems
Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis
A mesoscale connectome of the mouse brain
Seung Wook Oh,Julie A. Harris,Lydia Ng,Brent Winslow,Nicholas Cain,Stefan Mihalas,Quanxin Wang,Chris Lau,Leonard Kuan,Alex M. Henry,Marty Mortrud,Benjamin Ouellette,Thuc Nghi Nguyen,Staci A. Sorensen,Clifford R. Slaughterbeck,Wayne Wakeman,Yang Li,David Feng,Anh Ho,Eric Nicholas,Karla E. Hirokawa,Phillip Bohn,Kevin M. Joines,Hanchuan Peng,Michael Hawrylycz,John W. Phillips,John G. Hohmann,Paul Wohnoutka,Charles R. Gerfen,Christof Koch,Amy Bernard,Chinh Dang,Allan R. Jones,Hongkui Zeng +33 more