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X-ray micro-computed tomography (μCT) was applied upon selected ophiolitic rock samples from various localities of the Vardar ophiolite outcrops in North Greece. Effectiveness of the μCT application was evaluated through this case study by comparing results with other state-of-the-art techniques (e.g., optical microscopy, mineral chemistry microanalyses, XRD and QEMSCAN) to provide suggestive methodologies for optimum characterization, geological modeling, and visualization of ophiolitic rocks. The research outcomes provide an innovative approach for accurate modal composition calculations, crystal structure and mineral distribution in a 3D perspective, by combining μCT results with mineral chemical analyses. The information obtained is critical for investigating ophiolitic rocks to resolve complex petrogenetic and post-magmatic phenomena, to identify fabrics related to deformation, and furthermore results can also be used for applied research purposes. The obtained μCT results suggest that distributions of mineral's grayscale values strongly rely on three key factors: (i) participation of mineral phases with distinct attenuation coefficient and/or density properties, (ii) coexistence of different mafic minerals or mafic with non-mafic phases, (iii) variability in their mineral chemistry. The ability to analyze and visualize the internal mineral constituents of ophiolitic rocks samples, through the combination of μCT and Energy-Dispersive X-ray spectroscopy (EDS), can lead to advanced 3D stereological rock fabric analyses, which is advantageous compared to 2D methodologies. The μCT allowed to perform rock fabric calculations (best-fit ellipsoids and with volume) upon specified grain size distributions to identify and characterize the 3D morphological properties of the participating crystals and their preferable orientation., (Copyright © 2022 Elsevier Ltd. All rights reserved.)