The present study reports a semiautomatic image analysis method for measuring the spatiotemporal dynamics of the vessel dilation that was fluorescently imaged with either confocal or two-photon microscope. With this method, arterial dilation induced by whisker stimulation was compared between cortical surface and parenchymal tissue in the vibrissae area of somatosensory cortex in awake Tie2-GFP mice in which the vascular endothelium had genetically expressed green fluorescent protein. We observed that a mean arterial diameter during a pre-stimulus baseline state was 39 ± 7, 19 ± 1, 16 ± 4, 17 ± 4, and 14 ± 3 μm at depths of 0, 100, 200, 300, and 400 μm, respectively. The stimulation-evoked dilation induced by mechanical whisker deflection (10 Hz for 5 s) was 3.4 ± 0.8, 1.8 ± 0.8, 1.8 ± 0.9, 1.6 ± 0.9, and 1.5 ± 0.6 μm at each depth, respectively. Consequently, no significant differences were observed for the vessel dilation rate between the cortical surface and parenchymal arteries: 8.8 %, 9.9 %, 10.9 %, 9.2 %, and 10.3 % relative to their baseline diameters, respectively. These preliminary results demonstrate that the present method is useful to further investigate the quantitative relationships between the spatiotemporally varying arterial tone and the associated blood flow changes in the parenchymal microcirculation to reveal the regulatory mechanism of the cerebral blood flow.