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众包显微镜图像中神经胶质瘤细胞注释的任务设计。

Task design for crowdsourced glioma cell annotation in microscopy images.

机构信息

Department of Neuropathology, Institute for Pathology, Hannover Medical School, Hannover, Germany.

Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany.

出版信息

Sci Rep. 2024 Jan 23;14(1):1965. doi: 10.1038/s41598-024-51995-8.


DOI:10.1038/s41598-024-51995-8
PMID:38263411
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10805723/
Abstract

Crowdsourcing has been used in computational pathology to generate cell and cell nuclei annotations for machine learning. Herein, we broaden its scope to the previously unsolved challenging task of glioma cell detection. This requires multiplexed immunofluorescence microscopy due to diffuse invasiveness and exceptional similarity between glioma cells and reactive astrocytes. In four pilot experiments, we iteratively developed a task design enabling high-quality annotations by crowdworkers on Amazon Mechanical Turk. We applied majority or weighted vote and validated them against ground truth in the final setting. On the base of a YOLO convolutional neural network architecture, we used these consensus labels for training with different image representations regarding colors, intensities, and immmunohistochemical marker combinations. A crowd of 712 workers defined aggregated point annotations in 235 images with an average [Formula: see text] score of 0.627 for majority vote. The networks resulted in acceptable [Formula: see text] scores up to 0.69 for YOLOv8 on average and indicated first evidence for transferability to images lacking tumor markers, especially in IDH-wildtype glioblastoma. Our work confirms feasibility of crowdsourcing to generate labels suitable for training of machine learning tools in the challenging and clinically relevant use case of glioma microenvironment.

摘要

众包已被用于计算病理学,以生成机器学习的细胞和细胞核注释。在此,我们将其范围扩大到以前未解决的具有挑战性的胶质瘤细胞检测任务。这需要使用多重免疫荧光显微镜,因为胶质瘤细胞具有弥漫性侵袭性和与反应性星形胶质细胞的高度相似性。在四个试点实验中,我们在亚马逊 Mechanical Turk 上通过众包人员迭代开发了一项任务设计,从而实现了高质量的注释。我们应用了多数投票或加权投票,并在最终设置中根据ground truth 进行了验证。基于 YOLO 卷积神经网络架构,我们使用这些共识标签针对不同的颜色、强度和免疫组织化学标记组合的图像表示进行了训练。712 名工作人员在 235 张图像中定义了聚合点注释,多数投票的平均[Formula: see text]得分为 0.627。对于平均而言,YOLOv8 的网络结果达到了可接受的[Formula: see text]分数,高达 0.69,并且表明了缺乏肿瘤标志物的图像的可转移性的初步证据,尤其是在 IDH 野生型胶质母细胞瘤中。我们的工作证实了众包生成适合机器学习工具训练的标签的可行性,这些标签适用于胶质瘤微环境这一具有挑战性和临床相关的应用案例。

相似文献

[1]
Task design for crowdsourced glioma cell annotation in microscopy images.

Sci Rep. 2024-1-23

[2]
Crowdsourcing for Machine Learning in Public Health Surveillance: Lessons Learned From Amazon Mechanical Turk.

J Med Internet Res. 2022-1-18

[3]
Crowdsourcing image annotation for nucleus detection and segmentation in computational pathology: evaluating experts, automated methods, and the crowd.

Pac Symp Biocomput. 2015

[4]
Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing.

J Med Internet Res. 2013-4-2

[5]
Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations.

PLoS Comput Biol. 2021-8

[6]
Improving Consensus Scoring of Crowdsourced Data Using the Rasch Model: Development and Refinement of a Diagnostic Instrument.

J Med Internet Res. 2017-6-20

[7]
Crowdsourcing of Histological Image Labeling and Object Delineation by Medical Students.

IEEE Trans Med Imaging. 2018-11-26

[8]
Gamified Crowdsourcing as a Novel Approach to Lung Ultrasound Data Set Labeling: Prospective Analysis.

J Med Internet Res. 2024-7-4

[9]
AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images.

IEEE Trans Med Imaging. 2016-2-11

[10]
Fine-Tuning Deep Learning by Crowd Participation.

IEEE Pulse. 2018

本文引用的文献

[1]
Lessons from a breast cell annotation competition series for school pupils.

Sci Rep. 2022-5-12

[2]
Deep Learning From Multiple Noisy Annotators as A Union.

IEEE Trans Neural Netw Learn Syst. 2023-12

[3]
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.

Nat Biotechnol. 2022-4

[4]
A Crowdsourced Consensus on Supratotal Resection Versus Gross Total Resection for Anatomically Distinct Primary Glioblastoma.

Neurosurgery. 2021-9-15

[5]
Methods to Determine and Analyze the Cellular Spatial Distribution Extracted From Multiplex Immunofluorescence Data to Understand the Tumor Microenvironment.

Front Mol Biosci. 2021-6-14

[6]
Machine learning for cell classification and neighborhood analysis in glioma tissue.

Cytometry A. 2021-12

[7]
Learning from crowds in digital pathology using scalable variational Gaussian processes.

Sci Rep. 2021-6-2

[8]
Quantitative assessment of inflammatory infiltrates in kidney transplant biopsies using multiplex tyramide signal amplification and deep learning.

Lab Invest. 2021-8

[9]
Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.

Nat Commun. 2021-3-10

[10]
The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis.

Comput Biol Med. 2021-1

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