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This invention comprises the SWITCH system (System-Wide control of Interaction Time and kinetics of Chemicals), to tightly control a broad range of chemical reactions in tissue processing and proteomic labeling. A SWITCH-On buffer facilitates chemical reactions between exogenous chemicals and endogenous biomolecules, and a SWTICH-Off buffer suppresses the reactions. These buffers can be used easily to turn tissue into a transparent, heat- and chemical-resistant, architecturally preserved, molecularly labeled structure without needing to fix it with traditional methods. SWITCH can be used to control the rate at which probes penetrate through tissue to label the molecules of interest; thus, it can be used to clear very thick tissue, such as an entire rat brain. The SWITCH system has been used to successfully pass postmortem human tissue through a minimum of 22 rounds of SWITCH labeling with more than 100 targets, all visualized at subcellular resolution. In addition, it has also been used successfully label myelinated axons in intact mouse brain hemispheres. Finally, it has been used successfully to label 1-mm-thick mouse brain blocks with antibodies. The fact that this system is inexpensive and experimentally simple allows for its implementation in most labs.