Tissue clearing protocols

This tutorial provides guidance for selecting and optimizing tissue-clearing protocols for specific samples and biological questions. In addition, instructions are provided for developing an imaging strategy and processing the resulting data.

A full-body nanobody-based immunolabeling and clearing method that renders mice transparent in 3 weeks, enhancing the signal of fluorescent proteins and allowing their reliable detection and quantification, at cellular resolution, within an entire body.

This protocol describes labeling, clearing, imaging and cellular-level three-dimensional image reconstruction of intact human organs achieved with the help of a novel tissue clearing and labeling technology and a commercially available microscope.

This protocol describes how to perform antigen retrieval and tissue clearing for volumetric imaging of whole organs, organoids and small organisms by using fast light-microscopic analysis of antibody-stained whole organs.

Transparent organs are obtained, with retained fluorescent protein signals, upon clearing by immersion in the appropriate CUBIC reagent. The positions of all the cells can be determined using the described software.

This protocol for clearing and high-resolution 3D imaging of entire organoids expressing fluorescence reporters or following immunolabeling enables confocal, super-resolution confocal, multiphoton and light-sheet microscopy to be performed.

Li et al. detail a protocol for clearing-enhanced 3D (Ce3D), a method for tissue clearing, multiplexed immunofluorescence, RNA FISH microscopy of whole-mount tissues/thick tissue slices, and quantitative image analysis with volumetric histocytometry.

This protocol describes how to fix, embed, clear and stain excised organs or whole organisms to create optically transparent samples. This versatile protocol is able to process a wide range of sample types for high-resolution imaging.

This protocol describes how to perform CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis), a simple and efficient method for organ clearing, imaging by light-sheet microscopy, and quantitative imaging analysis.

CLARITY enables the chemical transformation of intact biological tissues into a hydrogel–tissue hybrid. The hybrid samples can be interrogated using light and macromolecular labels, whilst retaining fine structure and native biological molecules.