Comprehensive Evaluation and Fine-Tuning of Foundational Cell Nuclei Segmentation Models in Renal Pathology
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Abstract
Accurate nuclei instance segmentation is essential for quantitative renal pathology, yet general-purpose models often struggle with low contrast, dense nuclei, complex morphology, and strong background staining. In this work, we extended a human-in-the-loop framework by combining 5,901 foundation-model-generated pseudo-labels from well-segmented cases (Easy), 860 newly expert-annotated unresolved challenging cases (Medium), and 198 expert-annotated consensus failure cases (Hard). These annotations, spanning different levels of segmentation difficulty, enabled the systematic evaluation of seven single-source and mixed-source fine-tuning strategies across nine cell segmentation model configurations. Fine-tuning improved all models, with Medium data included in seven of the nine best-performing strategies. LSP-DETR achieved the highest F1 score of 0.8725 with Hard-only fine-tuning, while StarDist showed the largest improvement, increasing from 0.7380 to 0.8332 with Medium-only fine-tuning. These findings show that annotations spanning multiple difficulty levels support effective model adaptation, although the optimal annotation composition remains model dependent.
