Charged-particle microbeams, developed to provide targeted irradiation of individual cells, and then of sub-cellular components, and then of 3-D tissues and now organisms, have been instrumental in challenging and changing long accepted paradigms of radiation action. However the potential of these valuable tools can be enhanced by integrating additional components with the direct ability to measure biological responses in real time, or to manipulate the cell, tissue or organism of interest under conditions where information gained can be optimized. The RARAF microbeam has recently undergone an accelerator upgrade, and been modified to allow for multiple microbeam irradiation laboratories. Researchers with divergent interests have expressed desires for particular modalities to be made available and ongoing developments reflect these desires. The focus of this review is on the design, incorporation and use of multiphoton and other imaging, micro-manipulation and single cell biosensor capabilities at RARAF. Additionally, an update on the status of the other biology oriented microbeams in the Americas is provided.