The concept of a "standardized brain" is familiar in modern functional neuro-imaging techniques including PET and fMRI, but it has never been adopted for optical imaging studies that deal with a regional cortical area rather than the whole brain. In this paper, we propose a "standardized barrel cortex" for rodents, and present a method for mapping optically detected neural activity onto the standard cortex. The standard cortex is defined as a set of simple cortical columns, which are modeled on the cytoarchitectonic patterns of cell aggregates in cortical layer IV of the barrel cortex. Referring to its underlying anatomical structure, the method warps the surface image of individual cortices to fit the standard cortex. The cortex is warped using a two-dimensional free-form deformation technique with direct manipulation. Since optical imaging provides a map of neural activity on the cortical surface, the warping consequently remaps it on the standard cortex. Data presented in this paper show that somatosensory evoked neural activity is successfully represented on the standardized cortex, suggesting that the combination of optical imaging with our method is a promising approach for investigating the functional architecture of the cortex.