In order to help discover how neural circuits implement brain functions, and how these computations go awry in brain disorders, our neurotechnology group and our collaborators invent technologies to enable the scalable, systematic observation and control of biological structures and processes in the living brain. We have developed a suite of genetically-encoded reagents that, when expressed in specific neuron types in the nervous system, enable their electrical activities to be precisely driven or silenced in response to millisecond timescale pulses of light. I will give an overview of these “optogenetic” tools, and discuss a number of new tools for neural activation and silencing that we are developing, including molecules with augmented amplitudes, improved expression, novel color sensitivities, and other unique capabilities. We have also developed hardware to enable complex and distributed neural circuits to be controlled in a 3-D fashion, and for the network-wide impact of a neural control event to be measured using distributed electrodes or fMRI. We have also devised robots for automated intracellular neural recording, thus enabling rapid integrative analyses of single cells in living brain. We explore how these tools can be used to enable systematic analysis of neural circuit functions that support emotion, cognition, sensation, and movement, and discuss how these tools can be translationally applied to both support the understanding of brain disorders and to empower new kinds of therapy.