A unified framework for the analysis of fluorescence data taken by a two-photon imaging system is presented. As in the processing of blood-oxygen-level-dependent signals of functional magnetic resonance imaging, the acquired functional images have to be co-registered with a structural brain atlas before delineating the regions activated by a given stimulus. The voxels whose calcium traces are highly correlated with the predicted responses are demarcated without the need for subjective reasoning. Experimental data acquired while presenting olfactory stimuli are used to demonstrate the efficacy of the proposed schemes. The results indicate that the functional images of a Drosophila individual can be normalized into a standard stereotactic space, and the expected brain regions can be delineated adequately. This framework provides an opportunity to enable the development of a Drosophila functional connectome database.