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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
专题类脑智能研究中心
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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