[2605.03144] NucEval: A Robust Evaluation Framework for Nuclear Instance Segmentation
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Computer Science > Computer Vision and Pattern Recognition
arXiv:2605.03144 (cs)
[Submitted on 4 May 2026]
Title:NucEval: A Robust Evaluation Framework for Nuclear Instance Segmentation
Authors:Amirreza Mahbod, Ramona Woitek, Jeanne Shen
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Abstract: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: this https URL.
Comments: 22 pages
Subjects:
Computer Vision and Pattern Recognition (cs.CV)
Cite as: arXiv:2605.03144 [cs.CV]
(or arXiv:2605.03144v1 [cs.CV] for this version)
https://doi.org/10.48550/arXiv.2605.03144
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arXiv-issued DOI via DataCite (pending registration)
Submission history
From: Amirreza Mahbod [view email] [v1] Mon, 4 May 2026 20:33:42 UTC (4,736 KB)
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