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arXiv · 2101.08910

Single Neuron Segmentation using Graph-based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images

Heng Wang·Yang Song·Chaoyi Zhang·Jianhui Yu·Siqi Liu·Hanchuan Peng·Weidong Cai
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Abstract

One of the critical steps in improving accurate single neuron reconstruction from three-dimensional (3D) optical microscope images is the neuronal structure segmentation. However, they are always hard to segment due to the lack in quality. Despite a series of attempts to apply convolutional neural networks (CNNs) on this task, noise and disconnected gaps are still challenging to alleviate with the neglect of the non-local features of graph-like tubular neural structures. Hence, we present an end-to-end segmentation network by jointly considering the local appearance and the global geometry traits through graph reasoning and a skeleton-based auxiliary loss. The evaluation results on the Janelia dataset from the BigNeuron project demonstrate that our proposed method exceeds the counterpart algorithms in performance.

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Heng Wang, Yang Song, Chaoyi Zhang, Jianhui Yu, Siqi Liu, Hanchuan Peng, Weidong Cai. 2021-01-22. Single Neuron Segmentation using Graph-based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images. https://arxiv.org/abs/2101.08910

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