Before beginning in vivo imaging experiments, first conduct a virus dilution study (steps 1–5). Next, transduce cells with the appropriate dilution of the viral construct and implant a microendoscope above the target neuron population (steps 6–45). After sufficient time has been allowed for the virus to express and the tissue to clear under the microendoscope, use the miniature, integrated microscope to check expression levels of Ca2+ indicator. If cells can be clearly visualized and there is an indication of dynamic changes in fluorescence activity, perform baseplate attachment surgery (steps 46–74). If required for behavioral experiments, habituate mice to procedures for attaching a baseplate and in vivo recordings (step 75). Once necessary surgical and habituation procedures have been completed, conduct in vivo imaging studies in freely behaving mice and extract data (steps 76–100).