Literature DB >> 31896771

Tissue clearing and its applications in neuroscience.

Hiroki R Ueda1,2, Ali Ertürk3,4,5, Kwanghun Chung6,7,8,9,10,11,12, Viviana Gradinaru13, Alain Chédotal14, Pavel Tomancak15,16, Philipp J Keller17.   

Abstract

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

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Year:  2020        PMID: 31896771      PMCID: PMC8121164          DOI: 10.1038/s41583-019-0250-1

Source DB:  PubMed          Journal:  Nat Rev Neurosci        ISSN: 1471-003X            Impact factor:   34.870


  170 in total

1.  Three-dimensional mapping of brain neuropils in the cockroach, Diploptera punctata.

Authors:  A S Chiang; Y C Liu; S L Chiu; S H Hu; C Y Huang; C H Hsieh
Journal:  J Comp Neurol       Date:  2001-11-05       Impact factor: 3.215

2.  Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury.

Authors:  Ali Ertürk; Christoph P Mauch; Farida Hellal; Friedrich Förstner; Tara Keck; Klaus Becker; Nina Jährling; Heinz Steffens; Melanie Richter; Mark Hübener; Edgar Kramer; Frank Kirchhoff; Hans Ulrich Dodt; Frank Bradke
Journal:  Nat Med       Date:  2011-12-25       Impact factor: 53.440

3.  Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.

Authors:  Etsuo A Susaki; Kazuki Tainaka; Dimitri Perrin; Hiroko Yukinaga; Akihiro Kuno; Hiroki R Ueda
Journal:  Nat Protoc       Date:  2015-10-08       Impact factor: 13.491

4.  Involvement of Ca(2+)-Dependent Hyperpolarization in Sleep Duration in Mammals.

Authors:  Fumiya Tatsuki; Genshiro A Sunagawa; Shoi Shi; Etsuo A Susaki; Hiroko Yukinaga; Dimitri Perrin; Kenta Sumiyama; Maki Ukai-Tadenuma; Hiroshi Fujishima; Rei-ichiro Ohno; Daisuke Tone; Koji L Ode; Katsuhiko Matsumoto; Hiroki R Ueda
Journal:  Neuron       Date:  2016-03-17       Impact factor: 17.173

5.  Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes.

Authors:  Nicolas Renier; Eliza L Adams; Christoph Kirst; Zhuhao Wu; Ricardo Azevedo; Johannes Kohl; Anita E Autry; Lolahon Kadiri; Kannan Umadevi Venkataraju; Yu Zhou; Victoria X Wang; Cheuk Y Tang; Olav Olsen; Catherine Dulac; Pavel Osten; Marc Tessier-Lavigne
Journal:  Cell       Date:  2016-05-26       Impact factor: 41.582

6.  Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels.

Authors:  Philbert S Tsai; John P Kaufhold; Pablo Blinder; Beth Friedman; Patrick J Drew; Harvey J Karten; Patrick D Lyden; David Kleinfeld
Journal:  J Neurosci       Date:  2009-11-18       Impact factor: 6.167

7.  ScaleS: an optical clearing palette for biological imaging.

Authors:  Hiroshi Hama; Hiroyuki Hioki; Kana Namiki; Tetsushi Hoshida; Hiroshi Kurokawa; Fumiyoshi Ishidate; Takeshi Kaneko; Takumi Akagi; Takashi Saito; Takaomi Saido; Atsushi Miyawaki
Journal:  Nat Neurosci       Date:  2015-09-14       Impact factor: 24.884

Review 8.  Hydrogel-Tissue Chemistry: Principles and Applications.

Authors:  Viviana Gradinaru; Jennifer Treweek; Kristin Overton; Karl Deisseroth
Journal:  Annu Rev Biophys       Date:  2018-05-20       Impact factor: 12.981

9.  Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography.

Authors:  Collin Kieffer; Mark S Ladinsky; Allen Ninh; Rachel P Galimidi; Pamela J Bjorkman
Journal:  Elife       Date:  2017-02-15       Impact factor: 8.140

10.  A platform for brain-wide imaging and reconstruction of individual neurons.

Authors:  Michael N Economo; Nathan G Clack; Luke D Lavis; Charles R Gerfen; Karel Svoboda; Eugene W Myers; Jayaram Chandrashekar
Journal:  Elife       Date:  2016-01-20       Impact factor: 8.140

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  110 in total

Review 1.  Tutorial: practical considerations for tissue clearing and imaging.

Authors:  Kurt R Weiss; Fabian F Voigt; Douglas P Shepherd; Jan Huisken
Journal:  Nat Protoc       Date:  2021-05-21       Impact factor: 13.491

2.  Elasticizing tissues for reversible shape transformation and accelerated molecular labeling.

Authors:  Taeyun Ku; Webster Guan; Nicholas B Evans; Chang Ho Sohn; Alexandre Albanese; Joon-Goon Kim; Matthew P Frosch; Kwanghun Chung
Journal:  Nat Methods       Date:  2020-05-18       Impact factor: 28.547

3.  Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy.

Authors:  Adele Moatti; Yuheng Cai; Chen Li; Tyler Sattler; Laura Edwards; Jorge Piedrahita; Frances S Ligler; Alon Greenbaum
Journal:  Biomed Opt Express       Date:  2020-10-08       Impact factor: 3.732

4.  In situ genome sequencing resolves DNA sequence and structure in intact biological samples.

Authors:  Andrew C Payne; Zachary D Chiang; Paul L Reginato; Edward S Boyden; Jason D Buenrostro; Fei Chen; Sarah M Mangiameli; Evan M Murray; Chun-Chen Yao; Styliani Markoulaki; Andrew S Earl; Ajay S Labade; Rudolf Jaenisch; George M Church
Journal:  Science       Date:  2020-12-31       Impact factor: 47.728

5.  Whole Murine Brain Imaging Based on Optical Elastic Scattering.

Authors:  Jian Ren; Brett E Bouma
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

6.  Application of a Tissue Clearing Method for the Analysis of Dopaminergic Axonal Projections.

Authors:  Kenta Yamauchi; Megumu Takahashi; Hiroyuki Hioki
Journal:  Methods Mol Biol       Date:  2021

7.  Large-scale, cell-resolution volumetric mapping allows layer-specific investigation of human brain cytoarchitecture.

Authors:  Irene Costantini; Giacomo Mazzamuto; Matteo Roffilli; Annunziatina Laurino; Filippo Maria Castelli; Mattia Neri; Giovanni Lughi; Andrea Simonetto; Erica Lazzeri; Luca Pesce; Christophe Destrieux; Ludovico Silvestri; Valerio Conti; Renzo Guerrini; Francesco Saverio Pavone
Journal:  Biomed Opt Express       Date:  2021-05-27       Impact factor: 3.732

Review 8.  CODEX multiplexed tissue imaging with DNA-conjugated antibodies.

Authors:  Sarah Black; Darci Phillips; John W Hickey; Julia Kennedy-Darling; Vishal G Venkataraaman; Nikolay Samusik; Yury Goltsev; Christian M Schürch; Garry P Nolan
Journal:  Nat Protoc       Date:  2021-07-02       Impact factor: 13.491

Review 9.  Recent advances in lineage tracing for the kidney.

Authors:  Yoshiharu Muto; Benjamin D Humphreys
Journal:  Kidney Int       Date:  2021-07-01       Impact factor: 10.612

Review 10.  Tissue clearing to examine tumour complexity in three dimensions.

Authors:  Jorge Almagro; Hendrik A Messal; May Zaw Thin; Jacco van Rheenen; Axel Behrens
Journal:  Nat Rev Cancer       Date:  2021-07-30       Impact factor: 60.716

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