SegET: Deep Neural Network with Rich Contextual Features for Cellular Structures Segmentation in Electron Tomography Image

Abstract: Electron tomography (ET) allows high-resolution reconstructions of macromolecular complexes at nearnative state. Cellular structures segmentation in the reconstruction data from electron tomographic images is often required for analyzing and visualizing biological structures, making it a powerful tool for quantitative descriptions of whole cell structures and understanding biological functions. However, these cellular structures are rather difficult to automatically separate or quantify from view owing to complex molecular environment and the limitations of reconstruction data of ET. In this paper, we propose a single end-to-end deep fully-convolutional semantic segmentation network dubbed SegET with rich contextual features which fully exploitsthe multi-scale and multi-level contextual information and reduces the loss of details of cellular structures in ET images. We trained and evaluated our network on the electron tomogram of the CTL Immunological Synapse from Cell Image library. Our results demonstrate that SegET can automatically segment accurately and outperform all other baseline methods on each individual structure in our ET dataset.