A optical system and imaging device provide simultaneous or sequential optogenetic stimulation of different locations within a biological sample and fluorescence imaging of the locations. The systems include an illumination array with multiple electrically addressable elements that select a spatial pattern of illumination, an optical fiber bundle with fibers coupled between the array element and target locations at the sample, a fluorescence illumination source, and an imaging system for measuring fluorescence returning from the target locations. The optical imaging devices include a housing and a sample connector configured for receiving a first optical fiber bundle connection including multiple optical fibers. The sample connector has an indexing feature to maintain a fixed relationship between the fibers and internal optical paths of the device. The imaging devices also include an indexed input connector to receive another fiber bundle that carries the stimulus pattern, and a fluorescence excitation input connector.