Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models
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arXiv
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| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866914071307091968 |
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| author | Wang, Runchen Guo, Junlin Lu, Siqi Deng, Ruining Lu, Zhengyi Zhu, Yanfan Yang, Yuechen Qu, Chongyu Wang, Yu Zhao, Shilin Chang, Catie Wilkes, Mitchell Yin, Mengmeng Yang, Haichun Huo, Yuankai |
| author_facet | Wang, Runchen Guo, Junlin Lu, Siqi Deng, Ruining Lu, Zhengyi Zhu, Yanfan Yang, Yuechen Qu, Chongyu Wang, Yu Zhao, Shilin Chang, Catie Wilkes, Mitchell Yin, Mengmeng Yang, Haichun Huo, Yuankai |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2510_01287 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models Wang, Runchen Guo, Junlin Lu, Siqi Deng, Ruining Lu, Zhengyi Zhu, Yanfan Yang, Yuechen Qu, Chongyu Wang, Yu Zhao, Shilin Chang, Catie Wilkes, Mitchell Yin, Mengmeng Yang, Haichun Huo, Yuankai Quantitative Methods Artificial Intelligence 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. |
| title | Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models |
| topic | Quantitative Methods Artificial Intelligence |
| url | https://arxiv.org/abs/2510.01287 |