Tissue clearing

Richardson, Douglas S.; Guan, Webster; Matsumoto, Katsuhiko; Pan, Chenchen; Chung, Kwanghun; Ertürk, Ali; Ueda, Hiroki R.; Lichtman, Jeff W.

doi:10.1038/s43586-021-00080-9

Cited by 86 publications

(100 citation statements)

References 171 publications

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“…Tissue clearing methods have evolved rapidly and have been applied to image 3-dimensional (3D) structures of tissues at single-cell resolution (Ueda et al 2020 ; Richardson et al 2021 ). Tissue clearing can be achieved by a combination of delipidation and matching the refractive index (RI) of tissues with that of the mounting medium.…”

Section: Introductionmentioning

confidence: 99%

Chemical fluorescence-based dye staining for 3-dimensional histopathology analysis

Kim

Choi

et al. 2022

Animal Cells and Systems

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Tissue clearing for 3-dimensional (3D) imaging is increasingly utilized in many biomedical applications, including the pathological examination of human biopsy specimens. Although many protocols offer rapid and efficient tissue clearing (>1 d), immunofluorescence labeling of thick specimens is a highly time-consuming process. The use of low molecular weight chemical dyes has potential benefits in terms of speed and quality of 3D labeling. Accordingly, we tested several chemical dyes to assess their potential applications in 3D imaging. The combination of SYTO 16 and eosin (S&E) was found to be a potential fluorescent version of the hematoxylin–eosin (H&E) stain. Furthermore, picrosirius red (for collagen), Congo red (for senile plaques), and fluorescent Nissl (for neurons in the normal brain or blood vessels in the injured brain) stains can be used alone or in combination with antibody labeling. As chemical labeling requires a relatively short incubation time (<1 d), fluorescent chemical dyes could expedite the 3D imaging process.

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Section: Introductionmentioning

confidence: 99%

Chemical fluorescence-based dye staining for 3-dimensional histopathology analysis

Kim

Choi

et al. 2022

Animal Cells and Systems

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“…Tissue clearing allows for light microscopy to observe the distribution of individual molecules throughout entire organs millimeters to centimeters in size. 1,2 This holds extraordinary promise for understanding human diseases, where the identification and characterization of abnormal structures is often an early step towards the development of clinical treatments. 3 Difficulties with antibody staining and labeling is common in traditional thin tissue section histology, but is dramatically amplified in large, cleared samples.…”

Section: Introductionmentioning

confidence: 99%

“…The tissue may also be blocked by incubating with serum or other agents to deactivate endogenous enzymes and reduce non-specific antibody staining. Finally, when labeling and imaging thick tissue, tissue clearing protocols are required and introduce several additional chemical treatments including chemical crosslinking, removal of undesired molecules from the tissue, and immersion in a solution that is refractive index matched to the processed tissue 2,13 .…”

Section: Introductionmentioning

confidence: 99%

Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue

Zwang

Bennett

Lysandrou

et al. 2022

Preprint

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Difficulty achieving complete, specific, and homogenous staining is a major bottleneck preventing the widespread use of tissue clearing techniques to image large volumes of human tissue. In this manuscript, we describe a procedure to rapidly design immunostaining protocols for antibody labeling of cleared brain tissue. We prepared libraries of .5-1.0 mm thick tissue sections that are fixed, pre-treated, and cleared via similar, but different procedures to optimize staining conditions for a panel of antibodies. Results from a library of mouse tissue correlate well with results from a similarly prepared library of human brain tissue, suggesting mouse tissue is an adequate substitute for protocol optimization. These data show that procedural differences do not influence every antibody-antigen pair in the same way, and minor changes can have deleterious effects, therefore, optimization should be conducted for each target. The approach outlined here will help guide researchers to successfully label a variety of targets, thus removing a major hurdle to accessing the rich 3D information available in large, cleared human tissue volumes.

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“…A systematic understanding of biological systems requires an unbiased investigation into entire vertebrate bodies, not just specific organs, at sub-cellular resolutions. [1][2][3] For instance, in developmental biology, a high spatial resolution is essential for discerning changes in subcellular structures during different developmental stages, whereas full spatial coverage is needed for organ morphogenesis analysis from a systematic perspective. 4 This type of high-resolution panoptic imaging is also crucial for researching nervous systems, as changes in cellular organelles or nanoscale neuronal structures must be observed across the entire body.…”

Section: Introductionmentioning

confidence: 99%

Nanoscale resolution imaging of the whole mouse embryos and larval zebrafish using expansion microscopy

Sim

et al. 2021

Preprint

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Nanoscale imaging of all anatomical structures over whole vertebrates is needed for a systematic understanding of human diseases, but this has not yet been achieved. Here, we demonstrate whole-ExM, which enables nanoscale imaging of all anatomical structures of whole zebrafish larvae by labeling the proteins of the larvae with fluorophores and expanding them four-fold. We first optimize the fluorophore selection and labeling procedure to visualize a broader range of anatomical structures. We then develop an expansion protocol for zebrafish larvae having calcified body parts. Through this process, we visualize the nanoscale details of diverse larvae organs, which have corresponding organ counterparts in humans, over the intact larvae. We show that whole-ExM retains the fluorescence signals of fluorescent proteins, and its resolution is high enough to visualize various structures that can be imaged only with electron microscopy. Whole-ExM would enable the nanoscale study of the molecular mechanisms of human diseases.

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Tissue clearing

Cited by 86 publications

References 171 publications

Chemical fluorescence-based dye staining for 3-dimensional histopathology analysis

Chemical fluorescence-based dye staining for 3-dimensional histopathology analysis

Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue

Nanoscale resolution imaging of the whole mouse embryos and larval zebrafish using expansion microscopy

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