Neural systems are complicated networks connected by a large number of neurons through gap junctions and synapses. 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 encoder-decoder network, which extracted segmentation features of neural cell bodies and cell nuclei 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 state-of-the-art performance on quality metrics. Finally, we visualized two intact neural cell bodies and cell nuclei to provide a close look into these fine structures.