Literature DB >> 33769689

A guidebook for DISCO tissue clearing.

Muge Molbay1,2,3, Zeynep Ilgin Kolabas1,2,4, Mihail Ivilinov Todorov1,2,4, Tzu-Lun Ohn1,2, Ali Ertürk1,2,5.   

Abstract

Histological analysis of biological tissues by mechanical sectioning is significantly time-consuming and error-prone due to loss of important information during sample slicing. In the recent years, the development of tissue clearing methods overcame several of these limitations and allowed exploring intact biological specimens by rendering tissues transparent and subsequently imaging them by laser scanning fluorescence microscopy. In this review, we provide a guide for scientists who would like to perform a clearing protocol from scratch without any prior knowledge, with an emphasis on DISCO clearing protocols, which have been widely used not only due to their robustness, but also owing to their relatively straightforward application. We discuss diverse tissue-clearing options and propose solutions for several possible pitfalls. Moreover, after surveying more than 30 researchers that employ tissue clearing techniques in their laboratories, we compiled the most frequently encountered issues and propose solutions. Overall, this review offers an informative and detailed guide through the growing literature of tissue clearing and can help with finding the easiest way for hands-on implementation.
© 2021 The Authors. Published under the terms of the CC BY 4.0 license.

Entities:  

Keywords:  3D imaging; DISCO; labeling; light sheet; tissue clearing

Year:  2021        PMID: 33769689      PMCID: PMC7995442          DOI: 10.15252/msb.20209807

Source DB:  PubMed          Journal:  Mol Syst Biol        ISSN: 1744-4292            Impact factor:   11.429


  100 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.  Single-Cell Lineage Tracing Reveals that Oriented Cell Division Contributes to Trabecular Morphogenesis and Regional Specification.

Authors:  Jingjing Li; Lianjie Miao; David Shieh; Ernest Spiotto; Jian Li; Bin Zhou; Antoni Paul; Robert J Schwartz; Anthony B Firulli; Harold A Singer; Guoying Huang; Mingfu Wu
Journal:  Cell Rep       Date:  2016-03-24       Impact factor: 9.423

4.  The effect of heparin on the early stages of blood coagulation.

Authors:  J R O'BRIEN
Journal:  J Clin Pathol       Date:  1960-03       Impact factor: 3.411

5.  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 6.  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

7.  Tridimensional visualization reveals direct communication between the embryo and glands critical for implantation.

Authors:  Jia Yuan; Wenbo Deng; Jeeyeon Cha; Xiaofei Sun; Jean-Paul Borg; Sudhansu K Dey
Journal:  Nat Commun       Date:  2018-02-09       Impact factor: 14.919

8.  Optimization of GFP Fluorescence Preservation by a Modified uDISCO Clearing Protocol.

Authors:  Yusha Li; Jianyi Xu; Peng Wan; Tingting Yu; Dan Zhu
Journal:  Front Neuroanat       Date:  2018-08-15       Impact factor: 3.856

9.  Exploiting Multi-Level Parallelism for Stitching Very Large Microscopy Images.

Authors:  Alessandro Bria; Massimo Bernaschi; Massimiliano Guarrasi; Giulio Iannello
Journal:  Front Neuroinform       Date:  2019-06-04       Impact factor: 4.081

10.  Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease.

Authors:  Brian Hsueh; Vanessa M Burns; Philip Pauerstein; Katherine Holzem; Li Ye; Kristin Engberg; Ai-Chi Wang; Xueying Gu; Harini Chakravarthy; H Efsun Arda; Gregory Charville; Hannes Vogel; Igor R Efimov; Seung Kim; Karl Deisseroth
Journal:  Sci Rep       Date:  2017-07-19       Impact factor: 4.379

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  11 in total

Review 1.  Fate-mapping mice: new tools and technology for immune discovery.

Authors:  Scarlett E Lee; Brian D Rudd; Norah L Smith
Journal:  Trends Immunol       Date:  2022-01-31       Impact factor: 16.687

Review 2.  3D imaging for driving cancer discovery.

Authors:  Ravian L van Ineveld; Esmée J van Vliet; Ellen J Wehrens; Maria Alieva; Anne C Rios
Journal:  EMBO J       Date:  2022-04-11       Impact factor: 14.012

Review 3.  Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling.

Authors:  Yoichi Minami; Yufei Yuan; Hiroki R Ueda
Journal:  Biophys Rev       Date:  2021-11-18

Review 4.  Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain.

Authors:  Kyra T Newmaster; Fae A Kronman; Yuan-Ting Wu; Yongsoo Kim
Journal:  Front Neuroanat       Date:  2022-01-14       Impact factor: 3.856

5.  Clearing-induced tisssue shrinkage: A novel observation of a thickness size effect.

Authors:  R C M Vulders; R C van Hoogenhuizen; E van der Giessen; P J van der Zaag
Journal:  PLoS One       Date:  2021-12-16       Impact factor: 3.240

Review 6.  Advances in studying whole mouse brain vasculature using high-resolution 3D light microscopy imaging.

Authors:  Hannah C Bennett; Yongsoo Kim
Journal:  Neurophotonics       Date:  2022-04-05       Impact factor: 4.212

7.  Growth factor dependency in mammary organoids regulates ductal morphogenesis during organ regeneration.

Authors:  Sounak Sahu; Mary E Albaugh; Betty K Martin; Nimit L Patel; Lisa Riffle; Susan Mackem; Joseph D Kalen; Shyam K Sharan
Journal:  Sci Rep       Date:  2022-05-03       Impact factor: 4.996

8.  Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging.

Authors:  Adele Moatti; Chen Li; Sasank Sivadanam; Yuheng Cai; James Ranta; Jorge A Piedrahita; Alan G Cheng; Frances S Ligler; Alon Greenbaum
Journal:  iScience       Date:  2022-06-30

9.  Long Preservation of AAV-Transduced Fluorescence by a Modified Organic Solvent-Based Clearing Method.

Authors:  Tao Lu; Munehisa Shinozaki; Narihito Nagoshi; Masaya Nakamura; Hideyuki Okano
Journal:  Int J Mol Sci       Date:  2022-08-25       Impact factor: 6.208

10.  A Straightforward Method for 3D Visualization of B Cell Clusters and High Endothelial Venules in Lymph Nodes Highlights Differential Roles of TNFRI and -II.

Authors:  Kim C M Jeucken; Jasper J Koning; Jan Piet van Hamburg; Reina E Mebius; Sander W Tas
Journal:  Front Immunol       Date:  2021-06-21       Impact factor: 7.561

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