An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks

doi:10.1142/S0219720017500159

	An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks
	Li, Weifu 1,2; Deng, Hao 2,3; Rao, Qiang2 ; Xie, Qiwei2 ; Chen, Xi2 ; Han, Hua2,4,5
刊名	JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
	2017-06-01
卷号	15 期号:3 页码:1750015
关键词	Atum-sem Membrane Enhancement Mitochondria Group-similarity
DOI	10.1142/S0219720017500159
文献子类	Article
英文摘要	It is possible now to look more closely into mitochondrial physical structures due to the rapid development of electron microscope (EM). Mitochondrial physical structures play important roles in both cellular physiology and neuronal functions. Unfortunately, the segmentation of mitochondria from EM images has proven to be a difficult and challenging task, due to the presence of various subcellular structures, as well as image distortions in the sophisticated background. Although the current state-of-the-art algorithms have achieved some promising results, they have demonstrated poor performances on these mitochondria which are in close proximity to vesicles or various membranes. In order to overcome these limitations, this study proposes explicitly modelling the mitochondrial double membrane structures, and acquiring the image edges by way of ridge detection rather than by image gradient. In addition, this study also utilizes group-similarity in context to further optimize the local misleading segmentation. Then, the experimental results determined from the images acquired by automated tape-collecting ultramicrotome scanning electron microscopy (ATUM-SEM) demonstrate the effectiveness of this study's proposed algorithm.
WOS关键词	ELECTRON-MICROSCOPY ; IMAGE SEGMENTATION ; CANCER ; RECONSTRUCTION ; SHAPE
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematical & Computational Biology
语种	英语
WOS记录号	WOS:000404061500009
资助机构	Special Program of Beijing Municipal Science & Technology Commission(Z161100000216146) ; Strategic Priority Research Program of the CAS(XDB02060001) ; National Science Foundation of China(61673381 ; Institute of Automation, CAS(Y3J2031DZ1) ; 61201050 ; 61306070)
内容类型	期刊论文
源URL	[http://ir.ia.ac.cn/handle/173211/15243]
专题	自动化研究所_类脑智能研究中心
作者单位	1.Hubei Univ, Fac Math & Stat, Wuhan 430062, Peoples R China 2.Chinese Acad Sci, Inst Automat, Beijing 100190, Peoples R China 3.Macau Univ Sci & Technol, Fac Informat Technol, Hefei 999078, Macau, Peoples R China 4.Univ Chinese Acad Sci, Future Technol Coll, Beijing 100190, Peoples R China 5.CBS Ctr Excellence Brain Sci & Intelligence Techn, Shanghai 200031, Peoples R China
推荐引用方式 GB/T 7714	Li, Weifu,Deng, Hao,Rao, Qiang,et al. An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks[J]. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY,2017,15(3):1750015.
APA	Li, Weifu,Deng, Hao,Rao, Qiang,Xie, Qiwei,Chen, Xi,&Han, Hua.(2017).An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks.JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY,15(3),1750015.
MLA	Li, Weifu,et al."An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks".JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 15.3(2017):1750015.