Leaf temperature is a physiological trait that can be used for monitoring plant water status. Nowadays, by means of thermography, canopy temperature can be remotely determined. In this sense, it is crucial to automatically process the images. In the present work, a methodology for the automatic analysis of frontal images taken on individual trees was developed. The procedure can be used when cameras take at the same time thermal and visible scenes, so it is not necessary to reference the images. In this way, during the processing in batch, no operator participated. The procedure was developed by means of a non supervised classification of the visible image from which the presence of sky and soil could be detected. In case of existence, a mask was performed for the extraction of intermediate pixels to calculate canopy temperature by means of the thermal image. At the same time, sunlit and shady leaves could be detected and isolated. Thus, the procedure allowed to separately determine canopy temperature either of the more exposed part of the canopy or of the shaded portion. The methodology developed was validated using images taken in several regulated deficit irrigation trials in Persimmon and two citrus cultivars (Clementina de Nules and Navel Lane-Late). Overall, results indicated that similar canopy temperatures were calculated either by means of the automatic process or the manual procedure. The procedure developed allows to drastically reduce the time needed for image analysis also considering that no operator participation was required. This tool will facilitate further investigations in course for assessing the feasibility of thermography for detecting plant water status in woody perennial crops with discontinuous canopies. Preliminary results reported indicate that the type of crop evaluated has an important influence in the results obtained from thermographic imagery. Thus, in Persimmon trees there were good correlations between canopy temperature and plant water status while, in Clementina de Nules and Navel Lane-Late citrus cultivars canopy temperature differences among trees could not be related with tree-to-tree variations in plant water status.