Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in beta-cells during insulin secretion

doi:10.1371/journal.pone.0265567

	Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in beta-cells during insulin secretion
	Li, Angdi1,2,3 ; Zhang, Xiangyi4 ; Singla, Jitin 6; White, Kate 6; Loconte, Valentina1,2 ; Hu, Chuanyang4 ; Zhang, Chuyu4 ; Li, Shuailin4 ; Li, Weimin1,2,3 ; Francis, John Paul 7; Wang, Chenxi1,2,3 ; Sali, Andrej 8; Sun, Liping1,2 ; He, Xuming4,5 ; Stevens, Raymond C.1,2,6
	2022-03-24
发表期刊	PLOS ONE (IF:2.9[JCR-2023],3.3[5-Year])
ISSN	1932-6203
卷号	17 期号:3
发表状态	已发表
DOI	10.1371/journal.pone.0265567
摘要	The mesoscale description of the subcellular organization informs about cellular mechanisms in disease state. However, applications of soft X-ray tomography (SXT), an important approach for characterizing organelle organization, are limited by labor-intensive manual segmentation. Here we report a pipeline for automated segmentation and systematic analysis of SXT tomograms. Our approach combines semantic and first-applied instance segmentation to produce separate organelle masks with high Dice and Recall indexes, followed by analysis of organelle localization based on the radial distribution function. We demonstrated this technique by investigating the organization of INS-1E pancreatic beta-cell organization under different treatments at multiple time points. Consistent with a previous analysis of a similar dataset, our results revealed the impact of glucose stimulation on the localization and molecular density of insulin vesicles and mitochondria. This pipeline can be extended to SXT tomograms of any cell type to shed light on the subcellular rearrangements under different drug treatments.
URL	查看原文
收录类别	SCI ; SCIE
语种	英语
资助项目	NIH["P41GM103445","R01GM083960","P41GM109824"] ; DOE's Office of Biological and Environmental Research[DE-AC02-5CH11231] ; National Natural Science Foundation of China[31950410543]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000780951300047
出版者	PUBLIC LIBRARY SCIENCE
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/176017
专题	信息科学与技术学院_硕士生 iHuman研究所_特聘教授组_Andrej Sali组 iHuman研究所_特聘教授组_Raymond Stevens组信息科学与技术学院_PI研究组_何旭明组生命科学与技术学院_博士生信息科学与技术学院_博士生
通讯作者	Sun, Liping; He, Xuming; Stevens, Raymond C.
作者单位	1.ShanghaiTech Univ, iHuman Inst, Shanghai, Peoples R China 2.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.ShanghaiTech Univ, Sch Informat Sci & Technol, Shanghai, Peoples R China 5.Shanghai Engn Res Ctr Intelligent Vis & Imaging, Shanghai, Peoples R China 6.Univ Southern Calif, Bridge Inst, Dept Biol Sci, Los Angeles, CA 90007 USA 7.Univ Southern Calif, USC Michelson Ctr Convergent Biosci, Bridge Inst, Dept Comp Sci, Los Angeles, CA 90007 USA 8.Univ Calif San Francisco, Dept Pharmaceut Chem, Dept Bioengn & Therapeut Sci, Calif Inst Quantitat Biosci, San Francisco, CA USA
第一作者单位	iHuman研究所; 生命科学与技术学院
通讯作者单位	iHuman研究所; 生命科学与技术学院; 信息科学与技术学院
第一作者的第一单位	iHuman研究所
推荐引用方式 GB/T 7714	Li, Angdi,Zhang, Xiangyi,Singla, Jitin,et al. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in beta-cells during insulin secretion[J]. PLOS ONE,2022,17(3).
APA	Li, Angdi.,Zhang, Xiangyi.,Singla, Jitin.,White, Kate.,Loconte, Valentina.,...&Stevens, Raymond C..(2022).Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in beta-cells during insulin secretion.PLOS ONE,17(3).
MLA	Li, Angdi,et al."Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in beta-cells during insulin secretion".PLOS ONE 17.3(2022).