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Abstract Diagnosing diseases heavily relies on cell pathology images, but the extensive data in each manual identification of relevant cells labor-intensive, especially in regions with a scarcity of qualified healthcare professionals. This study aims to develop an intelligent system to enhance the diagnostic accuracy of cytopathology images by addressing image noise and segmentation issues, thereby improving the efficiency of medical professionals in disease diagnosis. We introduced an innovative system combining a self-supervised algorithm, SDN, for image denoising with data enhancement and image segmentation using the UPerMVit model. The UPerMVit model’s novel attention mechanisms and modular architecture provide higher accuracy and lower computational complexity than traditional methods. The proposed system effectively reduces image noise and accurately segments annotated images, highlighting cellular structures relevant to medical staff. This enhances diagnostic accuracy and aids in the accurate identification of pathological cells. Our intelligent system offers a reliable tool for medical professionals, improving diagnostic efficiency and accuracy in cytopathologic image analysis. It provides significant technical support in regions lacking adequate medical expertise.