Analyzing and repairing biological systems, such as the brain, requires tools for systematically mapping, dynamically observing, and dynamically controlling these systems. We are discovering new molecular principles to enable such technologies. For example, we discovered that one can physically magnify biological specimens by synthesizing dense networks of swellable polymer throughout them, and then chemically processing the specimens to isotropically swell them. This method, which we call expansion microscopy, enables ordinary microscopes to do nanoimaging. As a second example, we serendipitously discovered that microbial rhodopsins, genetically expressed in neurons, could enable their electrical activity to be precisely controlled in response to light. These molecules, now called optogenetic tools, enable causal assessment of how neurons contribute to behaviors and pathological states, and are yielding new candidate treatment strategies for brain diseases. Finally, in order to reveal relationships between different molecular signals within a cell, we are developing spatial and temporal multiplexing strategies that enable many signals to be imaged at once in the same living cell. Scientifically, we are focusing on the application of these tools to collect ground truth-oriented data for the worm C. elegans and the larval zebrafish, with the goal of creating biologically accurate computer simulations of entire brains.