An Effective Encoder-Decoder Network for Neural Cell Bodies and Cell Nucleus Segmentation of EM Images

Neural systems are complicated networks connected by a large number of neurons through gap junctions and synapse. At present, for electron microscopy connectomics research, neuron structure recognition algorithms mostly focus on synapses, dendrites, axons and mitochondria, etc. However, effective methods for automatic recognition of neuronal cell bodies are rare. In this paper, we proposed an effective encoderdecoder network, which extracted segmentation features of neural cell bodies and cell nucleus by the modified residual network and pyramid module. The framework is capable of merging multi-scale contextual information and generating efficient segmentation results by integrating multilevel features. We applied this proposed network on two segmentation tasks for electron microscope (EM) images and compared it with other promising methods as U-Net and deeplab v3+. The results demonstrated that our method achieved the state-of-the-art performance on quality metrics. Finally, we visualized two intact neural cell bodies and cell nucleus to provide a close look into these fine structures.