Clearing, labeling and expansion techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information without disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of new such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. I will provide an overview and comparisons of existing clearing, labeling and expansion techniques with the emphasis on CLARITY, stochastic electrotransport and SWITCH, introduce new techniques that we are developing and and discuss challenges and opportunities for the investigations of intact biological systems.