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Synchrotron Radiation (SR) X-Ray micro-Computed Tomography (μCT) enables magnified images that might be used as a non-invasive and non-destructive technique with a high space resolution for the qualitative and quantitative analysis of images. The research on applications of segmentation algorithms to SR-μCT is an open problem, due to the interesting and well-known characteristics of SR images for visualization, such as the high resolution, high brilliance and the phase contrast effect. We describe the application of the Energy Minimization via Graph Cuts algorithm (EMvGC) with swap move for the segmentation of SR-μCT images acquired at the Elettra Laboratory (Trieste, Italy). The EMvGC algorithm represents state-of-art segmentation algorithm which is fast and accurate, with outstanding results in several areas of computer vision, presenting an enormous potential of application in SR-μCT imaging.