A Unified Low-level Foundation Model for Enhancing Pathology Image Quality

Ziyi Liu; Zhe Xu; Jiabo Ma; Wenqaing Li; Junlin Hou; Fuxiang Huang; Xi Wang; Ronald Cheong Kin Chan; Terence Tsz Wai Wong; Hao Chen

arXiv · 2509.01071

A Unified Low-level Foundation Model for Enhancing Pathology Image Quality

Ziyi Liu·Zhe Xu·Jiabo Ma·Wenqaing Li·Junlin Hou·Fuxiang Huang·Xi Wang·Ronald Cheong Kin Chan·Terence Tsz Wai Wong·Hao Chen

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Abstract

Foundation models have revolutionized computational pathology by achieving remarkable success in high-level diagnostic tasks, yet the critical challenge of low-level image enhancement remains largely unaddressed. Real-world pathology images frequently suffer from degradations such as noise, blur, and low resolution due to slide preparation artifacts, staining variability, and imaging constraints, while the reliance on physical staining introduces significant costs, delays, and inconsistency. Although existing methods target individual problems like denoising or super-resolution, their task-specific designs lack the versatility to handle the diverse low-level vision challenges encountered in practice. To bridge this gap, we propose the first unified Low-level Pathology Foundation Model (LPFM), capable of enhancing image quality in restoration tasks, including super-resolution, deblurring, and denoising, as well as facilitating image translation tasks like virtual staining (H&E and special stains), all through a single adaptable architecture. Our approach introduces a contrastive pre-trained encoder that learns transferable, stain-invariant feature representations from 190 million unlabeled pathology images, enabling robust identification of degradation patterns. A unified conditional diffusion process dynamically adapts to specific tasks via textual prompts, ensuring precise control over output quality. Trained on a curated dataset of 87,810 whole slied images (WSIs) across 34 tissue types and 5 staining protocols, LPFM demonstrates statistically significant improvements (p<0.01) over state-of-the-art methods in most tasks (56/66), achieving Peak Signal-to-Noise Ratio (PSNR) gains of 10-15% for image restoration and Structural Similarity Index Measure (SSIM) improvements of 12-18% for virtual staining.

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Ziyi Liu, Zhe Xu, Jiabo Ma, Wenqaing Li, Junlin Hou, Fuxiang Huang, Xi Wang, Ronald Cheong Kin Chan, Terence Tsz Wai Wong, Hao Chen. 2025-09-01. A Unified Low-level Foundation Model for Enhancing Pathology Image Quality. https://arxiv.org/abs/2509.01071

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