In order to improve brain dysfunction such as mental disease, it is necessary to clarify the mechanism of activity in the brain. To clarify the relationship between the brain region and the neurotransmitter is important for elucidating the brain. Especially investigating the relationship between serotonin and hippocampus leads to elucidate of the mechanism of depression and sleep. The technique called optogenetics enabled only specific cells to be manipulated by light stimulation in recent years. This technique is a useful technique for clarifying the function of the brain. Because instead of stimulating multiple cells such as electrical stimulation, optogenetics can stimulate only specific cells, so that its function can be clarified. This study focused on neurotransmitter serotonin and the brain region called the hippocampus. For these purpose we can clarify the relationship between serotonin and hippocampus by manipulating serotonin neural activity using optogenetics while invasively measuring the ventral hippocampus of the mouse. In addition, identification of pyramidal cell layer is necessary to clarify hippocampal activity. Currently, visual estimation is performed based on the histology that dissected the brain, it still has a problem. Now this technique can't estimate ambiguous of the brain part and measure in an online manner. For this problem, we focus on the clarity of the brain part estimation when we used optogenetics. Therefore, we could estimate the pyramidal cell layer of the hippocampus by analyzing nerve activity and thought that the effect of serotonin activation or suppression on the hippocampus could be clarified. As a result, we showed that pyramidal cell layer can be identified by using principal component analysis, and could clarify the variation of nerve activity in the pyramidal cell layer of hippocampus during serotonin operation.