Fig. 1

Flowchart of compatible staining and imaging techniques for CLARITY-treated post mortem human brain tissue. Independent of type of fixation, e.g., perfusion-fixed versus exclusively immersion-fixed, or total fixation time, tissue samples can be embedded or cut directly on a vibratome. After CLARITY treatment, consisting of hydrogel polymerization with a consecutive SDS-based clearing step, fluorescence- or chromogen (e.g., 3,3’-diaminobenzidine (DAB))-based staining with a variety of cellular and synaptic markers can be performed. In addition, non-immuno-based Nissl staining is also compatible with CLARITY. Imaging can be performed with fluorescence microscopy (confocal or super-resolution microscopy) or with conventional light microscopy in case of DAB and Nissl staining. Primary and secondary antibodies as well as DAPI can be de-stained with the clearing solution, allowing for multiple staining rounds