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一个用于黑色素瘤细胞核和组织分割的新型数据集,带有基线细胞核分割和组织分割基准。

A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks.

作者信息

Schuiveling Mark, Liu Hong, Eek Daniel, Breimer Gerben E, Suijkerbuijk Karijn P M, Blokx Willeke A M, Veta Mitko

机构信息

Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands.

Medical Image Analysis, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands.

出版信息

Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf011.


DOI:10.1093/gigascience/giaf011
PMID:39970004
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11837757/
Abstract

BACKGROUND: Melanoma is an aggressive form of skin cancer in which tumor-infiltrating lymphocytes (TILs) are a biomarker for recurrence and treatment response. Manual TIL assessment is prone to interobserver variability, and current deep learning models are not publicly accessible or have low performance. Deep learning models, however, have the potential of consistent spatial evaluation of TILs and other immune cell subsets with the potential of improved prognostic and predictive value. To make the development of these models possible, we created the Panoptic Segmentation of nUclei and tissue in advanced MelanomA (PUMA) dataset and assessed the performance of several state-of-the-art deep learning models. In addition, we show how to improve model performance further by using heuristic postprocessing in which nuclei classes are updated based on their tissue localization. RESULTS: The PUMA dataset includes 155 primary and 155 metastatic melanoma hematoxylin and eosin-stained regions of interest with nuclei and tissue annotations from a single melanoma referral institution. The Hover-NeXt model, trained on the PUMA dataset, demonstrated the best performance for lymphocyte detection, approaching human interobserver agreement. In addition, heuristic postprocessing of deep learning models improved the detection of noncommon classes, such as epithelial nuclei. CONCLUSION: The PUMA dataset is the first melanoma-specific dataset that can be used to develop melanoma-specific nuclei and tissue segmentation models. These models can, in turn, be used for prognostic and predictive biomarker development. Incorporating tissue and nuclei segmentation is a step toward improved deep learning nuclei segmentation performance. To support the development of these models, this dataset is used in the PUMA challenge.

摘要

背景:黑色素瘤是一种侵袭性皮肤癌,其中肿瘤浸润淋巴细胞(TILs)是复发和治疗反应的生物标志物。手动TIL评估容易出现观察者间的差异,并且当前的深度学习模型无法公开获取或性能较低。然而,深度学习模型有潜力对TILs和其他免疫细胞亚群进行一致的空间评估,具有提高预后和预测价值的潜力。为了使这些模型的开发成为可能,我们创建了晚期黑色素瘤细胞核和组织全景分割(PUMA)数据集,并评估了几种最先进的深度学习模型的性能。此外,我们展示了如何通过使用启发式后处理进一步提高模型性能,在该后处理中,细胞核类别根据其组织定位进行更新。 结果:PUMA数据集包括来自单个黑色素瘤转诊机构的155个原发性和155个转移性黑色素瘤苏木精和伊红染色的感兴趣区域,带有细胞核和组织注释。在PUMA数据集上训练的Hover-NeXt模型在淋巴细胞检测方面表现最佳,接近人类观察者间的一致性。此外,深度学习模型的启发式后处理提高了对非常见类别的检测,如上皮细胞核。 结论:PUMA数据集是第一个可用于开发黑色素瘤特异性细胞核和组织分割模型的黑色素瘤特异性数据集。这些模型反过来可用于预后和预测生物标志物的开发。纳入组织和细胞核分割是朝着提高深度学习细胞核分割性能迈出的一步。为了支持这些模型的开发,该数据集被用于PUMA挑战赛。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/3dcbdfae85dc/giaf011fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/bf4627dd5cb6/giaf011fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/3030dc05b373/giaf011fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/2b52d8992d70/giaf011fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/837329d5ca44/giaf011fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/0b0c7c1713a5/giaf011fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/93157ceadf5c/giaf011fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/3dcbdfae85dc/giaf011fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/bf4627dd5cb6/giaf011fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/3030dc05b373/giaf011fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/2b52d8992d70/giaf011fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/837329d5ca44/giaf011fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/0b0c7c1713a5/giaf011fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/93157ceadf5c/giaf011fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/57b0/11837757/3dcbdfae85dc/giaf011fig7.jpg

相似文献

[1]
A novel dataset for nuclei and tissue segmentation in melanoma with baseline nuclei segmentation and tissue segmentation benchmarks.

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[2]
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引用本文的文献

[1]
Simplified Artificial Intelligence Terminology for Pathologists.

Diagnostics (Basel). 2025-7-3

[2]
Machine learning to detect melanoma exploiting nuclei morphology and Spatial organization.

Sci Rep. 2025-7-1

[3]
Lightweight Evolving U-Net for Next-Generation Biomedical Imaging.

Diagnostics (Basel). 2025-4-28

本文引用的文献

[1]
Baseline tumor-infiltrating lymphocyte patterns and response to immune checkpoint inhibition in metastatic cutaneous melanoma.

Eur J Cancer. 2024-9

[2]
A panoptic segmentation dataset and deep-learning approach for explainable scoring of tumor-infiltrating lymphocytes.

NPJ Breast Cancer. 2024-6-28

[3]
Towards a general-purpose foundation model for computational pathology.

Nat Med. 2024-3

[4]
NuInsSeg: A fully annotated dataset for nuclei instance segmentation in H&E-stained histological images.

Sci Data. 2024-3-14

[5]
Clinical and translational attributes of immune-related adverse events.

Nat Cancer. 2024-4

[6]
Inflamed immune phenotype predicts favorable clinical outcomes of immune checkpoint inhibitor therapy across multiple cancer types.

J Immunother Cancer. 2024-2-14

[7]
Metrics reloaded: recommendations for image analysis validation.

Nat Methods. 2024-2

[8]
Deep learning model improves tumor-infiltrating lymphocyte evaluation and therapeutic response prediction in breast cancer.

NPJ Breast Cancer. 2023-8-30

[9]
Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer.

J Pathol. 2023-8

[10]
Deep learning-based scoring of tumour-infiltrating lymphocytes is prognostic in primary melanoma and predictive to PD-1 checkpoint inhibition in melanoma metastases.

EBioMedicine. 2023-7

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