Sean Yanik, Hang Yu, Nattawat Chaiyawong, Opeoluwa Adewale-Fasoro, Luciana Ribeiro Dinis, Ravi Kumar Narayanasamy, Elizabeth C Lee, Ariel Lubonja, Bowen Li, Stefan Jaeger, Prakash Srinivasan
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引用次数: 0
摘要
啮齿类疟疾模型是重要的临床前抗疟和疫苗测试工具。在这些模型中评估治疗效果通常需要人工计数受寄生虫感染的红细胞(iRBCs),这是一个耗时的过程,而且不同个体和实验室的计数结果可能不一致。我们开发了一种基于机器学习 (ML) 的易用软件 Malaria Screener R,通过自动计数啮齿动物体内的疟原虫 iRBC,加快了此类研究的进度并实现了标准化。该软件可以处理任何配备照相机的显微镜拍摄的吉氏染色血涂片图像。它具有直观的图形用户界面,便于图像处理和结果可视化。该软件是作为桌面应用程序开发的,可在标准的 Windows 和 MacOS 计算机上处理图像。作者之前创建的一个 ML 模型专门用于计算感染恶性疟原虫的人类红细胞,但在计算感染疟原虫的小鼠红细胞时表现不佳。我们利用该模型,加载了预训练的权重,并用新收集的数据对算法进行了训练,以计算受尤利疟原虫和伯热疟原虫感染的小鼠红细胞。这一新模型可靠地测量了尤利疟原虫和贝氏疟原虫寄生虫血症(R2 = 0.9916)。在使用独立显微镜进行寄生虫计数的子类别中,该模型达到了世卫组织能力级别 1。可靠的血期寄生虫血症自动分析将有助于各实验室在易于获取的体内疟疾模型中对新型疫苗和抗疟药物进行快速、一致的评估。
Application of Machine Learning in a Rodent Malaria Model for Rapid, Accurate, and Consistent Parasite Counts.
Rodent malaria models serve as important preclinical antimalarial and vaccine testing tools. Evaluating treatment outcomes in these models often requires manually counting parasite-infected red blood cells (iRBCs), a time-consuming process, which can be inconsistent between individuals and laboratories. We have developed an easy-to-use machine learning (ML)-based software, Malaria Screener R, to expedite and standardize such studies by automating the counting of Plasmodium iRBCs in rodents. This software can process Giemsa-stained blood smear images captured by any camera-equipped microscope. It features an intuitive graphical user interface that facilitates image processing and visualization of the results. The software has been developed as a desktop application that processes images on standard Windows and MacOS computers. A previous ML model created by the authors designed to count Plasmodium falciparum-infected human RBCs did not perform well counting Plasmodium-infected mouse RBCs. We leveraged that model by loading the pretrained weights and training the algorithm with newly collected data to target Plasmodium yoelii- and Plasmodium berghei-infected mouse RBCs. This new model reliably measured both P. yoelii and P. berghei parasitemia (R2 = 0.9916). Additional rounds of training data to incorporate variances due to length of Giemsa staining and type of microscopes, etc., have produced a generalizable model, meeting WHO competency level 1 for the subcategory of parasite counting using independent microscopes. Reliable, automated analyses of blood-stage parasitemia will facilitate rapid and consistent evaluation of novel vaccines and antimalarials across laboratories in an easily accessible in vivo malaria model.
期刊介绍:
The American Journal of Tropical Medicine and Hygiene, established in 1921, is published monthly by the American Society of Tropical Medicine and Hygiene. It is among the top-ranked tropical medicine journals in the world publishing original scientific articles and the latest science covering new research with an emphasis on population, clinical and laboratory science and the application of technology in the fields of tropical medicine, parasitology, immunology, infectious diseases, epidemiology, basic and molecular biology, virology and international medicine.
The Journal publishes unsolicited peer-reviewed manuscripts, review articles, short reports, images in Clinical Tropical Medicine, case studies, reports on the efficacy of new drugs and methods of treatment, prevention and control methodologies,new testing methods and equipment, book reports and Letters to the Editor. Topics range from applied epidemiology in such relevant areas as AIDS to the molecular biology of vaccine development.
The Journal is of interest to epidemiologists, parasitologists, virologists, clinicians, entomologists and public health officials who are concerned with health issues of the tropics, developing nations and emerging infectious diseases. Major granting institutions including philanthropic and governmental institutions active in the public health field, and medical and scientific libraries throughout the world purchase the Journal.
Two or more supplements to the Journal on topics of special interest are published annually. These supplements represent comprehensive and multidisciplinary discussions of issues of concern to tropical disease specialists and health issues of developing countries