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基于微生物分类特征提取的多类显微镜图像分类自动化

Automation of Multi-Class Microscopy Image Classification Based on the Microorganisms Taxonomic Features Extraction.

作者信息

Samarin Aleksei, Savelev Alexander, Toropov Aleksei, Dozortseva Aleksandra, Kotenko Egor, Nazarenko Artem, Motyko Alexander, Narova Galiya, Mikhailova Elena, Malykh Valentin

机构信息

Higher School of Digital Culture, ITMO University, St. Petersburg 197101, Russia.

Faculty of Radio Engineering and Telecommunications, St. Petersburg Electrotechnical University "LETI", St. Petersburg 197022, Russia.

出版信息

J Imaging. 2025 Jun 18;11(6):201. doi: 10.3390/jimaging11060201.

Abstract

This study presents a unified low-parameter approach to multi-class classification of microorganisms (micrococci, diplococci, streptococci, and bacilli) based on automated machine learning. The method is designed to produce interpretable taxonomic descriptors through analysis of the external geometric characteristics of microorganisms, including cell shape, colony organization, and dynamic behavior in unfixed microscopic scenes. A key advantage of the proposed approach is its lightweight nature: the resulting models have significantly fewer parameters than deep learning-based alternatives, enabling fast inference even on standard CPU hardware. An annotated dataset containing images of four bacterial types obtained under conditions simulating real clinical trials has been developed and published to validate the method. The results (Precision = 0.910, Recall = 0.901, and F1-score = 0.905) confirm the effectiveness of the proposed method for biomedical diagnostic tasks, especially in settings with limited computational resources and a need for feature interpretability. Our approach demonstrates performance comparable to state-of-the-art methods while offering superior efficiency and lightweight design due to its significantly reduced number of parameters.

摘要

本研究提出了一种基于自动化机器学习的统一低参数方法,用于对微生物(微球菌、双球菌、链球菌和杆菌)进行多类分类。该方法旨在通过分析微生物的外部几何特征(包括细胞形状、菌落组织以及在未固定微观场景中的动态行为)来生成可解释的分类描述符。所提出方法的一个关键优势在于其轻量级特性:生成的模型比基于深度学习的替代方案具有显著更少的参数,即使在标准CPU硬件上也能实现快速推理。已开发并发布了一个包含在模拟真实临床试验条件下获得的四种细菌类型图像的带注释数据集,以验证该方法。结果(精确率 = 0.910,召回率 = 0.901,F1分数 = 0.905)证实了所提出方法在生物医学诊断任务中的有效性,特别是在计算资源有限且需要特征可解释性的环境中。我们的方法展示了与最先进方法相当的性能,同时由于其显著减少的参数数量而具有更高的效率和轻量级设计。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/97f6/12194502/abcec73a81ea/jimaging-11-00201-g001.jpg

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