Deep Learning and Shapes Similarity for Joint Segmentation and Tracing single Neurons in SEM images

	Deep Learning and Shapes Similarity for Joint Segmentation and Tracing single Neurons in SEM images
	Rao Q(饶强); Xiao C(肖驰); Han H(韩华); Shen LJ(沈丽君); Chen X(陈曦); Xie QW(谢启伟)
	2017-04
会议名称	SPIE Medical Imaging
会议日期	2017-2-10
会议地点	美国奥兰多
摘要	Extracting the structure of single neurons is critical for understanding how they function within the neural circuits. Recent developments in microscopy techniques, and the widely recognized need for openness and standardization provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons. In order to look into the fine structure of neurons, we use the Automated Tape-collecting Ultra Microtome Scanning Electron Microscopy (ATUM-SEM) to get images sequence of serial sections of animal brain tissue that densely packed with neurons. Different from other neuron reconstruction method, we propose a method that enhances the SEM images by detecting the neuronal membranes with deep convolutional neural network (DCNN) and segments single neurons by active contour with group shape similarity. We joint the segmentation and tracing together and they interact with each other by alternate iteration that tracing aids the selection of candidate region patch for active contour segmentation while the segmentation provides the neuron geometrical features which improve the robustness of tracing. The tracing model mainly relies on the neuron geometrical features and is updated after neuron being segmented on the every next section. Our method enables the reconstruction of neurons of the drosophila mushroom body which is cut to serial sections and imaged under SEM. Our method provides an elementary step for the whole reconstruction of neuronal networks.
关键词	Deep Convolutional Neural Network Active Contour Neuron Reconstruction Membrane Detection Probability Map Neuron Tracing
学科领域	模式识别与智能系统
收录类别	EI
文献类型	会议论文
条目标识符	http://ir.ia.ac.cn/handle/173211/14645
专题	脑图谱与类脑智能实验室_微观重建与智能分析
作者单位	中国科学院自动化研究所
第一作者单位	中国科学院自动化研究所
推荐引用方式 GB/T 7714	Rao Q,Xiao C,Han H,et al. Deep Learning and Shapes Similarity for Joint Segmentation and Tracing single Neurons in SEM images[C],2017.

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