Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models

Runchen Wang; Junlin Guo; Siqi Lu; Ruining Deng; Zhengyi Lu; Yanfan Zhu; Yuechen Yang; Chongyu Qu; Yu Wang; Shilin Zhao; Catie Chang; Mitchell Wilkes; Mengmeng Yin; Haichun Yang; Yuankai Huo

arXiv · 2510.01287

Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models

Runchen Wang·Junlin Guo·Siqi Lu·Ruining Deng·Zhengyi Lu·Yanfan Zhu·Yuechen Yang·Chongyu Qu·Yu Wang·Shilin Zhao·Catie Chang·Mitchell Wilkes·Mengmeng Yin·Haichun Yang·Yuankai Huo

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Abstract

Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated early-generation AI cell foundation models in this domain, the effectiveness of recent cell foundation models remains unclear. In this study, we benchmark advanced AI cell foundation models (2025), including CellViT++ variants and Cellpose-SAM, against three widely used cell foundation models developed prior to 2024, using a diverse large-scale set of kidney image patches within a human-in-the-loop rating framework. We further performed fusion-based ensemble evaluation and model agreement analysis to assess the segmentation capabilities of the different models. Our results show that CellViT++ [Virchow] yields the highest standalone performance with 40.3% of predictions rated as "Good" on a curated set of 2,091 challenging samples, outperforming all prior models. In addition, our fused model achieves 62.2% "Good" predictions and only 0.4% "Bad", substantially reducing segmentation errors. Notably, the fusion model (2025) successfully resolved the majority of challenging cases that remained unaddressed in our previous study. These findings demonstrate the potential of AI cell foundation model development in renal pathology and provide a curated dataset of challenging samples to support future kidney-specific model refinement.

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Runchen Wang, Junlin Guo, Siqi Lu, Ruining Deng, Zhengyi Lu, Yanfan Zhu, Yuechen Yang, Chongyu Qu, Yu Wang, Shilin Zhao, Catie Chang, Mitchell Wilkes, Mengmeng Yin, Haichun Yang, Yuankai Huo. 2025-10-01. Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models. https://arxiv.org/abs/2510.01287

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