A miniaturized microscope provides the combined capability for simultaneous or sequential optogenetic stimulation of light sensitive ion channels with the capability for fluorescence imaging of fluorescent proteins for applications requiring simultaneous optical stimulation and monitoring of cell activity. The microscope includes a dual illumination output coupling for providing illumination to two different regions within the sample and/or two different illumination source inputs and a dual transmission band optical filter to clean two different bands of light that are separately available for optogenetic stimulation and fluorescence imaging.
