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Meat and bone meal is the main food transmission chain of Bovine Spongiform Encephalopathy. The research on the detection method of meat and bone meal in feed has been one of the key tasks in the field of feed safety in the world. In view of the differences in the microscopic lacunae of bone powders from aquatic and terrestrial animals, a method of Micro-CT in-situ three-dimensional visualization of the lacunae of bone particles of different species was proposed. Taking fish, bovine, porcine and chicken bone particles as research objects, Bruker Skyscan 1275 Micro-CT was used to optimize scanning and reconstruction conditions of each sample on the basis of scanning condition optimization. Global, Otsu, K-means clustering, Adaptive mean-C and Adaptive median-C were compared for the segmentation effect of bone particle microscopic lacunar imaging. The optimized Micro-CT scanning conditions were as follows: voltage 80kV, current 125μA, image resolution 8μm, rotation step 0.20°, exposure time 46 ms and scanning 360°. Smoothing 1, Post-Alignment 0, Ring-Artifacts 3, and Beam-hardening 30% were used for three-dimensional reconstruction. The local adaptive mean method had the best imaging effect of bone particles, and its optimal parameters WS was 5, C was 0. The results of Micro-CT in-situ three-dimensional visualization of the lacunae structure of bone particles from different animal sources were in good agreement with the results of microscope standard method. The results provided a method for rapid and nondestructive discriminant analysis of aquatic and terrestrial animals feed.