Our understanding of the aetiology and functional changes of brain diseases is restricted by the inaccessibility of the brain. To address existing technological limitations, the EU-funded DEEPER project proposes to generate tools for imaging and manipulating neuronal activity in the deep brain. The tools under development include high-efficiency molecular sensors, probes for cell monitoring, microscopes and microendoscopes that offer unprecedented resolution, sensitivity and depth of focus. DEEPER will provide insight into the molecular and cellular dysfunctions associated with specific neurological and psychiatric disorders such as schizophrenia, autism and Alzheimer's disease.