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使用大模型的数字病理学任务驱动框架。

Task-driven framework using large models for digital pathology.

作者信息

Yu Jiahui, Ma Tianyu, Chen Feng, Zhang Jing, Xu Yingke

机构信息

Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China.

Innovation Center for Smart Medical Technologies and Devices, Binjiang Institute of Zhejiang University, Hangzhou, China.

出版信息

Commun Biol. 2024 Dec 4;7(1):1619. doi: 10.1038/s42003-024-07303-1.

DOI:10.1038/s42003-024-07303-1
PMID:39632974
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11618297/
Abstract

Microscopy is an indispensable tool for collecting biomedical information in pathological diagnosis, but manual annotation, measurement and interpretation are labor-intensive and costly. Here, we propose a task-driven framework powered by large models that excel in visual analysis and real-time control, paving the way for the next generation of microscopes. We achieve proof-of-concept success on clinical tasks, specifically in adaptive analysis of H&E-stained liver tissue slides. This work demonstrates the advanced capabilities for future digital pathology, setting a new standard for intelligent, efficient, and real-time analysis in clinical applications.

摘要

显微镜检查是病理诊断中收集生物医学信息不可或缺的工具,但人工注释、测量和解读既费力又昂贵。在此,我们提出了一个由在视觉分析和实时控制方面表现出色的大模型驱动的任务驱动框架,为下一代显微镜铺平了道路。我们在临床任务上取得了概念验证的成功,特别是在对苏木精-伊红染色的肝组织切片进行自适应分析方面。这项工作展示了未来数字病理学的先进能力,为临床应用中的智能、高效和实时分析树立了新的标准。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5702/11618297/53337ae9f2c8/42003_2024_7303_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5702/11618297/acb12cd27d25/42003_2024_7303_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5702/11618297/53337ae9f2c8/42003_2024_7303_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5702/11618297/acb12cd27d25/42003_2024_7303_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5702/11618297/53337ae9f2c8/42003_2024_7303_Fig2_HTML.jpg

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本文引用的文献

1
Semi-Supervised Instance Segmentation in Whole Slide Images via Dense Spatial Variability Enhancing.通过增强密集空间变异性实现全切片图像中的半监督实例分割
IEEE J Biomed Health Inform. 2024 Jul 31;PP. doi: 10.1109/JBHI.2024.3436099.
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Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective.重新审视半监督医学图像分割:基于方差缩减的视角
Adv Neural Inf Process Syst. 2023 Dec;36:9984-10021.
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Vision-language foundation model for echocardiogram interpretation.用于超声心动图解释的视觉-语言基础模型。
Nat Med. 2024 May;30(5):1481-1488. doi: 10.1038/s41591-024-02959-y. Epub 2024 Apr 30.
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Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration.为基于荧光显微镜的可泛化图像恢复的基础模型进行预训练。
Nat Methods. 2024 Aug;21(8):1558-1567. doi: 10.1038/s41592-024-02244-3. Epub 2024 Apr 12.
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An open-source, high-resolution, automated fluorescence microscope.一款开源、高分辨率的自动化荧光显微镜。
Elife. 2024 Mar 4;12:RP89826. doi: 10.7554/eLife.89826.
6
A visual-language foundation model for pathology image analysis using medical Twitter.一种使用医学推特进行病理学图像分析的视觉语言基础模型。
Nat Med. 2023 Sep;29(9):2307-2316. doi: 10.1038/s41591-023-02504-3. Epub 2023 Aug 17.
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Smart microscopes of the future.未来的智能显微镜。
Nat Methods. 2023 Jul;20(7):962-964. doi: 10.1038/s41592-023-01912-0.
8
Local-to-global spatial learning for whole-slide image representation and classification.基于局部到全局的空间学习的全切片图像表示和分类。
Comput Med Imaging Graph. 2023 Jul;107:102230. doi: 10.1016/j.compmedimag.2023.102230. Epub 2023 Apr 22.
9
Effect of vessels that encapsulate tumor clusters (VETC) on the prognosis of different stages of hepatocellular carcinoma after hepatectomy.包裹肿瘤簇的血管(VETC)对肝癌切除术后不同分期患者预后的影响。
Dig Liver Dis. 2023 Sep;55(9):1288-1294. doi: 10.1016/j.dld.2023.03.008. Epub 2023 Apr 9.
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Cellpose 2.0: how to train your own model.Cellpose 2.0:如何训练自己的模型。
Nat Methods. 2022 Dec;19(12):1634-1641. doi: 10.1038/s41592-022-01663-4. Epub 2022 Nov 7.