A beginner's guide to tissue clearing

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.

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

Figure 1. Young rat central nervous system - uDISCO technique

An example of a very large sample imaged after tissue clearing. The central nervous system of a young rat was stained with a dye that labels the vasculature and cleared with the uDISCO technique, which uses organic solvents. The image is a composite of many images acquired with a light-sheet microscope. Insets show magnified views of subareas of the sample and arrowheads point to specific identifiable blood vessels. Modified from Pan et al., 2016.

Figure 2. 100 μm slice of mouse brain - See DB2 technique

An example of a small sample that benefits from tissue clearing. A 100 μm slice of brain tissue where a subset of neurons strongly express YFP was cleared with the SeeDB2 method, which is based on a high RI aqueous solution. This sample was imaged using Airyscan superresolution confocal microscopy. Note that very fine details can be discerned deep in the sample. Modified from Ke et al., 2016.