基于原子力显微镜和改进残差神经网络的细胞识别

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of structural biology Pub Date : 2023-09-01 DOI:10.1016/j.jsb.2023.107991
Junxi Wang , Mingyan Gao , Lixin Yang , Yuxi Huang , Jiahe Wang , Bowei Wang , Guicai Song , Zuobin Wang
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引用次数: 0

摘要

细胞识别方法在细胞生物学和医学领域都有很高的应用需求,而基于原子力显微镜(AFM)的细胞识别方法显示出很大的应用价值。细胞的力学性能或形态差异已被频繁用于检测细胞是否癌变,但这种检测方法并不能成为癌细胞检测的通用手段,传统的人工特征提取方法也有其局限性。在这项工作中,我们提出了一种基于细胞物理性质的分析方法和深度学习方法来识别细胞类型。利用多尺度卷积融合、注意机制和深度可分离卷积对残差神经网络进行改进,优化特征提取,降低运行成本。该方法对采集的细胞进行AFM成像,并利用优化后的卷积神经网络对处理后的图像进行分析。采用该方法对两组细胞(HL-7702和SMMC-7721, SGC-7901和GES-1)的识别结果表明,结合细胞表面形态、黏附和杨氏模量的数据集识别率更高,且最优分辨率数据集的识别率更高。我们的研究表明,使用深度学习技术识别细胞的物理特性可以作为细胞信息自动分析的通用和有效的方法。
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Cell recognition based on atomic force microscopy and modified residual neural network

Cell recognition methods are in high demand in cell biology and medicine, and the method based on atomic force microscopy (AFM) shows a great value in application. The difference in mechanical properties or morphology of cells has been frequently used to detect whether cells are cancerous, but this detection method cannot be a general means for cancer cell detection, and the traditional artificial feature extraction method also has its limitations. In this work, we proposed an analytic method based on the physical properties of cells and deep learning method for recognizing cell types. The residual neural network used for recognition was modified by multi-scale convolutional fusion, attention mechanism and depthwise separable convolution, so as to optimize feature extraction and reduce operation costs. In the method, the collected cells were imaged by AFM, and the processed images were analyzed by the optimized convolutional neural network. The recognition results of two groups of cells (HL-7702 and SMMC-7721, SGC-7901 and GES-1) by this method show that the recognition rate of dataset with the combination of cell surface morphology, adhesion and Young's modulus is higher, and the recognition rate of the dataset with optimal resolution is higher. Our study indicated that the recognition of physical properties of cells using deep learning technology can serve as a universal and effective method for the automated analysis of cell information.

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来源期刊
Journal of structural biology
Journal of structural biology 生物-生化与分子生物学
CiteScore
6.30
自引率
3.30%
发文量
88
审稿时长
65 days
期刊介绍: Journal of Structural Biology (JSB) has an open access mirror journal, the Journal of Structural Biology: X (JSBX), sharing the same aims and scope, editorial team, submission system and rigorous peer review. Since both journals share the same editorial system, you may submit your manuscript via either journal homepage. You will be prompted during submission (and revision) to choose in which to publish your article. The editors and reviewers are not aware of the choice you made until the article has been published online. JSB and JSBX publish papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure. Techniques covered include: • Light microscopy including confocal microscopy • All types of electron microscopy • X-ray diffraction • Nuclear magnetic resonance • Scanning force microscopy, scanning probe microscopy, and tunneling microscopy • Digital image processing • Computational insights into structure
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