Literature DB >> 28082099

A beginner's guide to tissue clearing.

Pablo Ariel1.   

Abstract

The last decade has seen a proliferation of tissue clearing methods that render large biological samples transparent and allow unprecedented three-dimensional views of enormous volumes of tissue. For a scientist wondering whether these methods will be useful to address their research problems, it can be bewildering to sort through the ever-increasing number of papers introducing new clearing methods. Here, I provide a concise summary for the novice describing what tissue clearing is, which research problems it can be applied to, how to decide on a clearing method, and where the field is headed in the future.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Optical clearing; Organoids; Tissue clearing; Whole organ imaging; Whole organism imaging

Mesh:

Substances:

Year:  2017        PMID: 28082099      PMCID: PMC5336404          DOI: 10.1016/j.biocel.2016.12.009

Source DB:  PubMed          Journal:  Int J Biochem Cell Biol        ISSN: 1357-2725            Impact factor:   5.085


  29 in total

1.  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

2.  Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent.

Authors:  Meng-Tsen Ke; Yasuhiro Nakai; Satoshi Fujimoto; Rie Takayama; Shuhei Yoshida; Tomoya S Kitajima; Makoto Sato; Takeshi Imai
Journal:  Cell Rep       Date:  2016-03-10       Impact factor: 9.423

Review 3.  Clarifying Tissue Clearing.

Authors:  Douglas S Richardson; Jeff W Lichtman
Journal:  Cell       Date:  2015-07-16       Impact factor: 41.582

4.  Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems.

Authors:  Evan Murray; Jae Hun Cho; Daniel Goodwin; Taeyun Ku; Justin Swaney; Sung-Yon Kim; Heejin Choi; Young-Gyun Park; Jeong-Yoon Park; Austin Hubbert; Margaret McCue; Sara Vassallo; Naveed Bakh; Matthew P Frosch; Van J Wedeen; H Sebastian Seung; Kwanghun Chung
Journal:  Cell       Date:  2015-12-03       Impact factor: 41.582

5.  Three-Dimensional Study of Alzheimer's Disease Hallmarks Using the iDISCO Clearing Method.

Authors:  Thomas Liebmann; Nicolas Renier; Karima Bettayeb; Paul Greengard; Marc Tessier-Lavigne; Marc Flajolet
Journal:  Cell Rep       Date:  2016-07-14       Impact factor: 9.423

6.  A rapid optical clearing protocol using 2,2'-thiodiethanol for microscopic observation of fixed mouse brain.

Authors:  Yuka Aoyagi; Ryosuke Kawakami; Hisayuki Osanai; Terumasa Hibi; Tomomi Nemoto
Journal:  PLoS One       Date:  2015-01-29       Impact factor: 3.240

7.  Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging.

Authors:  Jun Li; Daniel M Czajkowsky; Xiaowei Li; Zhifeng Shao
Journal:  Sci Rep       Date:  2015-05-27       Impact factor: 4.379

8.  Uncovering the Number and Clonal Dynamics of Mesp1 Progenitors during Heart Morphogenesis.

Authors:  Samira Chabab; Fabienne Lescroart; Steffen Rulands; Navrita Mathiah; Benjamin D Simons; Cédric Blanpain
Journal:  Cell Rep       Date:  2015-12-24       Impact factor: 9.423

9.  ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging.

Authors:  Eunsoo Lee; Jungyoon Choi; Youhwa Jo; Joo Yeon Kim; Yu Jin Jang; Hye Myeong Lee; So Yeun Kim; Ho-Jae Lee; Keunchang Cho; Neoncheol Jung; Eun Mi Hur; Sung Jin Jeong; Cheil Moon; Youngshik Choe; Im Joo Rhyu; Hyun Kim; Woong Sun
Journal:  Sci Rep       Date:  2016-01-11       Impact factor: 4.379

10.  Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences.

Authors:  Li Ye; William E Allen; Kimberly R Thompson; Qiyuan Tian; Brian Hsueh; Charu Ramakrishnan; Ai-Chi Wang; Joshua H Jennings; Avishek Adhikari; Casey H Halpern; Ilana B Witten; Alison L Barth; Liqun Luo; Jennifer A McNab; Karl Deisseroth
Journal:  Cell       Date:  2016-05-26       Impact factor: 41.582

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  34 in total

1.  Tissue Optical Clearing for Biomedical Imaging: From In Vitro to In Vivo.

Authors:  Tingting Yu; Dongyu Li; Dan Zhu
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

Review 2.  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

3.  Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network.

Authors:  Drew Friedmann; Albert Pun; Eliza L Adams; Jan H Lui; Justus M Kebschull; Sophie M Grutzner; Caitlin Castagnola; Marc Tessier-Lavigne; Liqun Luo
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-01       Impact factor: 11.205

4.  Combined iDISCO and CUBIC tissue clearing and lightsheet microscopy for in toto analysis of the adult mouse ovary†.

Authors:  Jennifer McKey; Lisa A Cameron; Devon Lewis; Iordan S Batchvarov; Blanche Capel
Journal:  Biol Reprod       Date:  2020-04-24       Impact factor: 4.285

Review 5.  Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy.

Authors:  Hiroki R Ueda; Hans-Ulrich Dodt; Pavel Osten; Michael N Economo; Jayaram Chandrashekar; Philipp J Keller
Journal:  Neuron       Date:  2020-05-06       Impact factor: 17.173

6.  Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy.

Authors:  Chen Li; Adele Moatti; Xuying Zhang; H Troy Ghashghaei; Alon Greenabum
Journal:  Biomed Opt Express       Date:  2021-07-22       Impact factor: 3.732

7.  F-CUBIC: a rapid optical clearing method optimized by quantitative evaluation.

Authors:  Lina Liu; Xianyuan Xia; Feng Xiang; Yufeng Gao; Xi Li; Hui Li; Wei Zheng
Journal:  Biomed Opt Express       Date:  2021-12-07       Impact factor: 3.732

8.  Hydrophobic and Hydrogel-Based Methods for Passive Tissue Clearing.

Authors:  Frank L Jalufka; Sun Won Min; Madison E Platt; Anna L Pritchard; Theodore E Margo; Alexandra O Vernino; Megan A Kirchhoff; Ryan T Massopust; Dylan A McCreedy
Journal:  Methods Mol Biol       Date:  2022

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.  Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes.

Authors:  Martha Campbell-Thompson; Shiue-Cheng Tang
Journal:  Front Endocrinol (Lausanne)       Date:  2021-04-26       Impact factor: 6.055

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