Figure 1: Tissue processing steps for optical clearing. After fixation by immersion in paraformaldehyde, an optional decolorization step for tissues that include high amounts of pigments (such as hemo- and myoglobin) is followed by whole organ immunostainings, preferably with red or far-red fluorophores. To streamline the image acquisition process, small organs can be embedded in agarose gel and imaged together. Thereafter, the samples undergo optical clearing in pH 9.0 adjusted and precooled (4°C) solvents in the dark. Then the cleared samples can be imaged or stored in the imaging solution, depending on the fluorophore stability. DRG: Dorsal root ganglia.