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Tissue processing is the technique by which fixed tissues are made suitable for embedding within a supportive medium such as paraffin, and consists of three sequential steps: dehydration, clearing, and infiltration. In most clinical and research settings, tissue processing is accomplished using an automated tissue processor, with or without microwave-assistance. Tissue clearing refers to a collection of techniques that render biological samples transparent. These techniques enable the deep imaging of large volumes of tissues using light microscopy approaches. Tissue clearing allows researchers to avoid time-consuming tissue sectioning approaches that can introduce artifacts and to examine biological tissues in their native, 3D state.