Diffuse optically tomography (DOT) approaches provide volumetric localization and better discrimination of the functional brain signals from the background and are crucial to establishing optical neuroimaging as a standard brain-mapping tool. We have developed instrumentation with improved performance characteristics that permits use of high-density DOT arrays. Our goal is to develop DOT for mapping activity throughout the outer surface of the human brain with centimeter resolution. We have also developed a method for mapping functional connectivity (fcDOT) within the brain using correlation analysis that allows us to isolate functional maps from resting-state measurements. These fcDOT methods provide a task-less approach to mapping brain function in populations that were previously difficult to research. Since our DOT system is portable, we have studied human behavior in our lab and also in the Neuronal Intensive Care Unit, Neonatal Intensive Care Unit, and Neonatal Nursery. We recently extended similar optical fc-mapping methods down to the scale of the mouse to provide a link between human fc-mapping and molecular mouse models. We have the ability to map functional connectivity in the mice using four hemodynamic contrasts: [HbO], [HbR], [HbT], and CBF. For small animal molecular imaging, our lab develops fluorescence tomography methods to provide quantitative molecular maps in vivo. Since fluorescence lifetime (FLT) of an optical probe is exquisitely sensitive to the local probe environment - through perturbation of excited state properties - we are developing DOT instrumentation which has the spectro-temporal capabilities needed for the FLT contrast.