Comprehensive Evaluation and Fine-Tuning of Foundational Cell Nuclei Segmentation Models in Renal Pathology

Background and Objective: Precise and scalable instance segmentation of cell nuclei is a fundamental prerequisite for computational pathology, yet gigapixel whole-slide images (WSIs) pose significant computational challenges. While patch-based processing is standard during training, existing methods are often limited to small tile sizes during inference due to architectural bottlenecks or reliance on computationally expensive post-processing for instance separation. We introduce a faster, scalable, and end-to-end framework capable of processing large-scale image tiles while accurately modeling biologically realistic overlapping nuclei. Methods: We propose LSP-DETR (Local Star Polygon DEtection TRansformer). The model represents nuclei as star-convex polygons and employs a lightweight transformer with linear complexity, enabling the processing of high-resolution images in a single forward pass. A novel radial distance loss accommodates annotation uncertainty, allowing the segmentation of overlapping nuclei to emerge naturally without explicit overlap labels. Results: LSP-DETR achieves state-of-the-art efficiency, with an inference time of 0.45 s/mm^2, a 3.2x speedup over StarDist, the next-fastest method. On PanNuke, the model achieves competitive accuracy (67.5 bPQ), while yielding an F$_1$-score of 0.964 in polygon overlap when evaluated against consensus annotations from two expert pathologists. Furthermore, it outperforms larger models such as LKCell in generalization robustness, reaching an F1-score of 85.0 on MoNuSeg. Conclusions: LSP-DETR bridges the gap between high-fidelity segmentation and practical clinical requirements by eliminating heuristic post-processing. By providing a scalable, linear-complexity solution that naturally handles overlaps between nuclei, this framework sets a new direction for efficient high-throughput WSI analysis in digital pathology.

In computational pathology, nuclear instance segmentation is a fundamental task with many downstream clinical applications. With the advent of deep learning, many approaches, including convolutional neural networks (CNNs) and vision transformers (ViTs), have been proposed for this task, along with both machine learning-based and non-machine learning-based pre- and post-processing techniques to further boost performance. However, one fundamental aspect that has received less attention is the evaluation pipeline. In this study, we identify four key issues associated with nuclear instance segmentation evaluation and propose corresponding solutions. Our proposed modifications, namely handling vague regions, score normalization, overlapping instances, and border uncertainty, are integrated into a unified framework called NucEval, which enables robust evaluation of nuclear instance segmentation. We evaluate this pipeline using the NuInsSeg dataset, which provides unique characteristics that make it particularly suitable for this study, as well as two additional external datasets, with three CNN- and ViT-based nuclear instance segmentation models, to demonstrate the impact of these modifications on instance segmentation metrics. The code, along with complete guidelines and illustrative examples, is publicly available at: https://github.com/masih4/nuc_eval.

Accurate classification of nuclei subtypes in histopathology images is critical for downstream tasks including tumor grading, immune infiltrate quantification, and prognosis prediction. Existing approaches rely on either convolutional or transformer-based encoders in isolation, limiting their ability to simultaneously capture fine-grained local texture and long-range spatial context. We present AMN (Adaptive Multi-Scale Nuclei Network), a dual-encoder segmentation framework that jointly leverages a Swin Transformer and a ResNet-50 feature pyramid, fused via a learned per-channel gating mechanism that dynamically weighs each encoder's contribution at every scale. AMN is trained with a multi-objective loss combining class-weighted focal loss, boundary-aware loss with positive-pixel emphasis, and a novel uncertainty-modulated classification term that suppresses overconfident erroneous predictions. Evaluated on the CoNIC benchmark across seven nuclei classes, AMN achieves a mean Dice of 0.82 and mean F1 of 0.68, with an F1 of 0.67 on the diagnostically challenging lymphocyte class. AMN outperforms eight baseline models spanning pure-CNN, pure-transformer, and recent hybrid architectures: U-Net, ResU-Net, DeepLabV3+, SegNet, ViT-Small, HmsU-Net, ConvFormer-UNet, and BEFUnet. Cross-dataset evaluation on MoNuSeg demonstrates strong generalization without retraining and validating the domain robustness of the learned representations.